| Name | Category | Organism | Program, Pipeline Name or Method Name | Source Name | Download link | |
|---|---|---|---|---|---|---|
| RepeatModeler Repeats | Genome structure | Soybean Cyst Nematode (v2) | Standard repeatmodeler and repeatmasker pipeline | H. glycines Genome Repeatmodeler Repeats | genome738sl.polished.mitofixed.fa_.out_sorted.gff_.gz | View on JBrowse |
| PA3 Transcriptome on susceptible and resistant soybean | Transcripts | Soybean Cyst Nematode (v2) | Trinity transcriptome with Gmap alignment | PA3 H. glycines transcriptome. Grown on susceptible and resistant soybean cultivars | nematode_transcripts_trinity.fasta_sorted_sorted.gff_.gz | View on JBrowse |
| Consensus Isoseq Transcriptome from PA3 and TN19 | Transcripts | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | H.glycines Isoseq Consensus isoforms | genome738sl.polished.consensus_isoforms_sorted.gff_.gz | View on JBrowse |
| NCBI Nucleotide Database Entries | Genes | Soybean Cyst Nematode (v2) | Gmap | NCBI Nucleotide entries for H. glycines | nucleotide_mapped_sorted_sorted.gff_.gz | View on JBrowse |
| NCBI EST Database Entries | Transcripts | Soybean Cyst Nematode (v2) | Gmap | NCBI EST entries for H. glycines | ests_mapped_sorted_gff_sorted_sorted.gff_.gz | View on JBrowse |
| Globodera rostochiensis Synteny with H.glycines | Genome structure | Soybean Cyst Nematode (v2) | Opscan ortholog calling, iadhore syntenic fragment | H. glycines synteny with G. rostochiensis genome (2016) | rostochiensis_syntenic_ribbons_txt_gfffixed_sorted.gff_.gz | View on JBrowse |
| Tandem Duplications | Genome structure | Soybean Cyst Nematode (v2) | Red Tandem used one scaffold at a time | H. glycines genomic tandem duplications | redtandemalljbrowsesort.bed.gz | View on JBrowse |
| High Confidence Horizontal Gene Transfers | Genes | Soybean Cyst Nematode (v2) | H. glycines high confidence HGT | H. glycines high confidence HGT | highconfhgtsorted.bed.gz | View on JBrowse |
| Meloidogyne Incognita Syntenic Regions | Genome structure | Soybean Cyst Nematode (v2) | Opscan ortholog calling, iadhore syntenic fragment | H. glycines synteny with M. incognita genome (2016) | incognita_syntenic_ribbons_txt_gff_sorted.gff_.gz | View on JBrowse |
| 80 Effector MEME->FIMO motifs | Genes | Soybean Cyst Nematode (v2) | MEME of 80 effector proteins, Genes with protein motifs found with FIMO | Effector Motifs from the 80 known motifs | fimogenessorted.bed.gz | View on JBrowse |
| 80 Published Effectors Nucleotide Alignment (GMAP) | Genes | Soybean Cyst Nematode (tn10) | Gmap Alignment of 80 Published Effectors | Nucleotide alignment with Gmap, default parameters | gmapeffectors.gff_.gz | View on JBrowse |
| Globodera ellingtonae Synteny with H.glycines | Genome structure | Soybean Cyst Nematode (v2) | Braker,Opscan ortholog calling, iadhore syntenic fragment | H. glycines synteny with G. ellingtonae genome (2017) | ellingtonae_syntenic_ribbons_txt_gff_sorted.gff_.gz | View on JBrowse |
| Meloidogyne hapla Synteny with H.glycines | Genome structure | Soybean Cyst Nematode (v2) | Opscan ortholog calling, iadhore syntenic fragment | H. glycines synteny with M. hapla genome (2008) | hapla_syntenic_ribbons_txt_gff_sorted.gff_.gz | View on JBrowse |
| Globodera pallida Synteny with H.glycines | Genome structure | Soybean Cyst Nematode (v2) | Opscan ortholog calling, iadhore syntenic fragment | H. glycines synteny with G. pallida genome (2017) | pallida_syntenic_ribbons_sorted_txt_gff_sorted.gff_.gz | View on JBrowse |
| LTR Retroelements | Genome structure | Soybean Cyst Nematode (v2) | LTRFinder, RepeatModeler, RepeatMasker, Bedtools Intersect | Full length LTR models merged with bedtools. Only those that overlap with repeatmodeler repeats, merged with bed | ltrretroelementsclassifiedcut_sorted.gff_.gz | View on JBrowse |
| DNA Transposons | Genome structure | Soybean Cyst Nematode (v2) | Inverted Repeat Finder,Repeatmodeler, RepeatMasker, Bedtools | Full length TIR pairs models merged with bedtools. Only those that overlap with repeatmodeler repeats, merged with bed | supportedirfmergeclassifiedscnbasesorted.bed.gz | View on JBrowse |
| Pre-parasitic J2 (PA3) Biorep 1 | Gene expression | Soybean Cyst Nematode (v2) | hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig | Pre-parasitic J2 (PA3) Biorep 1 | sortedppj2_pa3_tagctt.bam.bw | View on JBrowse |
| Helitrons | Genome structure | Soybean Cyst Nematode (v2) | Helitron Scanner | HelitronScanner default on H. glycines genome | helitronnamedsorted.bed.gz | View on JBrowse |
| Genes with promoters containing DOG-box motifs | Genes | Soybean Cyst Nematode (v2) | MEME to find Dog Box, BLAST to align GS-like effectors | H.glycines Dog-box genes | dorsal-likegenessorted.bed.gz | View on JBrowse |
| SNPs across 15 populations of H.glycines | Molecular markers (QTL) | Soybean Cyst Nematode (v2) | GATK Best Practices: BWA-mem, Picard, GATK | SNPs called from 15 populations of H. glycines | sortedrenamed.combined_variants.vcf.gz | View on JBrowse |
| Alignment of 80 published known effector genes (gff3) | Genes | Soybean Cyst Nematode (v2) | Gmap alignment with default parameters | 80 Known effectors Thomas Baum Lab | test2.gz | View on JBrowse |
| Falcon Assembled Pacbio RS II subreads (pReads) | Genome structure | Soybean Cyst Nematode (v2) | Blasr mapping of Pacbio preads to H.glycines genome | Pacbio pread mapping to genome | preads2genomegff.gz | View on JBrowse |
| Circular Consensus Pacbio RS II subreads (CCS Reads) | Genome structure | Soybean Cyst Nematode (v2) | Blasr mapping of CCS Pacbio reads | circular consensus reads assembled with smrtanalysis_2.3.0.140936. | ccs2genome.gff_.gz | View on JBrowse |
| Camtech Raw Pacbio RS II subreads | Genome structure | Soybean Cyst Nematode (v2) | Blasr mapping of raw Pacbio subreads | Raw Pacbio subreads (TN10) | subreads2genome.gff_.gz | View on JBrowse |
| W82_PA3_Eggs Isoseq reads | Gene expression | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | IDX1 Isoseq Baum/Severin | sortedidx1_isoforms_present.bed.gz | View on JBrowse |
| W82_PA3_J2/J3 Isoseq reads | Gene expression | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | IDX2 Isoseq Baum/Severin | sortedidx2_isoforms_present.bed.gz | View on JBrowse |
| W82_PA3_J4/Adult Isoseq reads | Gene expression | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | IDX3 Isoseq Baum/Severin | sortedidx3_isoforms_present.bed.gz | View on JBrowse |
| W82_TN19_Eggs Isoseq reads | Gene expression | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | IDX4 Isoseq Baum/Severin | sortedidx4_isoforms_present.bed.gz | View on JBrowse |
| W82_TN19_J4/Adult Isoseq reads | Gene expression | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | IDX5 Isoseq Baum/Severin | sortedidx5_isoforms_present.bed.gz | View on JBrowse |
| W82_TN19_J2/J3 | Gene expression | Soybean Cyst Nematode (v2) | SmartPortal, Gmap | IDX6 Isoseq Baum/Severin | sortedidx6_isoforms_present.bed.gz | View on JBrowse |
| Mitochondrial Genes | Genes | Soybean Cyst Nematode (v2) | mitos webserver alternative flatworm | From genome assembly | mitochondria.gff3.gz | View on JBrowse |
| parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 | Gene expression | Soybean Cyst Nematode (v2) | hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig | parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 | sortedpj2_s63_tgacca.bam.bw | View on JBrowse |
| Parasitic J2 (PA3) Forrest (Resistant Soybean) Biorep 1 | Gene expression | Soybean Cyst Nematode (v2) | hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig | parasitic J2 (PA3) Race 3 Forrest (Resistant soybean cultivar) Biorep 1 | sortedpj2_race3_forrest.bam.bw | View on JBrowse |
| Parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 2 | Gene expression | Soybean Cyst Nematode (v2) | hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig | parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 | sortedpj2_s63_ttaggc.bam.bw | View on JBrowse |
| Pre-parasitic J2 (PA3) Biorep 2 | Gene expression | Soybean Cyst Nematode (v2) | hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig | Pre-parasitic J2 (PA3) Biorep 2 | sortedppj2_pa3_atcacg.bam.bw | View on JBrowse |
| Repeat Explorer of TN20 | Genome structure | Soybean Cyst Nematode (v2) | RepeatExplorer2, GMAP | SRR3924425 | nononsensehashes_sorted.gff_.gz | View on JBrowse |
| Annotated Gene Models Heterodera Glycines (updated v2) | Genes | Soybean Cyst Nematode (v2) | Ortholog based Manual Annotations | Baum/Severin Labs | reworkedfunctionalaugustus_sorted_gff0.gz | View on JBrowse |
| Predicted Proteins from V2 Gene Models | Genes | Soybean Cyst Nematode (v2) | braker gene prediction, gff2fasta | From genome assembly | finalaugustus.pep_.fasta | |
| Annotated Braker Gene Models IPRSCAN | Genes | Soybean Cyst Nematode (v2) | Interproscan, Swissprot, Uniref | Baum/Severin Labs | annotatedcorrectlyaugustus_sorted77.gff_.gz | View on JBrowse |
| Globodera Ellingtonae Gene Predictions | Other | multispecies | Hisat2, Braker | Baum/Severin Labs, GCA_001723225.1, SRR3162514 | globoderaellingtonaegenepredictions.gff_.gz | |
| Trinity Transcripts form Gardner et al 2017 | Transcripts | Soybean Cyst Nematode (v2) | Gmap alignment | NCBI Bioproject PRJNA415980 | scngenome.gfzz01.1_sorted.gff_.gz | View on JBrowse |
| Alignments of genes producing secreted proteins | Genes | Soybean Cyst Nematode (v2) | Braker genes, SignalP | Genes with N terminal secretion signals, and lacking transmembrane domains | reworkedfunctionalaugustussecreted_sorted.gff_.gz | View on JBrowse |
| Transcripts of genes producing secreted proteins | Transcripts | Soybean Cyst Nematode (v2) | Braker genes, SignalP and Tmhmm | Baum/Severin Labs | secretedtranscripts.fasta | |
| Fasta sequences of the 80 published effector genes | Transcripts | Soybean Cyst Nematode (v2) | Collected from literature | Baum/Severin Labs | effector.fasta | |
| Input Transcriptome Assemblies to Final Prediction | Genes | Soybean Cyst Nematode (tn10) | masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks | Masonbrink | orderedmergingtestscn.gff3.resortfixed.gff_.gz | View on JBrowse |
| Published Effectors via protein-protein alignment | Genes | Soybean Cyst Nematode (tn10) | Diamond Alignment of 80 Published Effectors | Protein protein alignment with Diamond, default parameters | diamondeffectors.gff3.gz | View on JBrowse |
| tn10 genes | Genes | Soybean Cyst Nematode (tn10) | Placeholder | Rick Masonbrink | tn10genome.gff3.gz | View on JBrowse |
| X12 genes | Genes | Soybean Cyst Nematode (X12v2) | Placeholder | Rick Masonbrink | x12genome_sorted.gff3.gz | View on JBrowse |
| Genomethreader Alignment of X12 Annotation | Genes | Soybean Cyst Nematode (tn10) | Genomethreader of Published Annotation | Liam et al Gene Models, Masonbrink alignment | x12genomethreader.gff_.gz | View on JBrowse |
| Repeatmasker | Genome structure | Soybean Cyst Nematode (tn10) | Repeatmodeler Prediction, Repeatmasker Annotation | Masonbrink | repeatmasker.gff_.gz | View on JBrowse |
| NCRNAs Mikado Prediction | Noncoding RNAs | Soybean Cyst Nematode (tn10) | mikado prediction of NCRNAs | Masonbrink | ncrnas.gff3.gz | View on JBrowse |
| EDTA Annotated Transposons | Genome structure | Soybean Cyst Nematode (tn10) | EDTA Extensive Denovo Transposon Annotator | Masonbrink | edtatransposons1.gff3.gz | View on JBrowse |
| Tandem Repeats Finder | Genome structure | Soybean Cyst Nematode (tn10) | Tandem Repeats Finder | Masonbrink | sortedtrf.bed.gz | View on JBrowse |
| SVIM TN10 Pacbio Structural Variants | Genome structure | Soybean Cyst Nematode (tn10) | minimap2 mapping and SVIM | Masonbrink | svimvariants.vcf.gz | View on JBrowse |
| TN10 SNPS/INDELS | Molecular markers (QTL) | Soybean Cyst Nematode (tn10) | Freebayes 1.1.0, bcftools 1.10.2 filter | Masonbrink | sortscngenome.tn10sm.vcf.gz | View on JBrowse |
| Ribosomal Genes | Genes | Soybean Cyst Nematode (tn10) | BLAST of nematode ribosomal genes from NCBI | Masonbrink | ribocoordsfix.bed.gz | View on JBrowse |
| TN10 H.glycines Pseudomolecule Assembly Sequence | Genome structure | Soybean Cyst Nematode (tn10) | Falcon, Falcon unzip, Dovetail genomics, Sspace, Juicer/3D-DNA, pilon | Masonbrink | scngenome.fasta | |
| TN10 H.glycines Pseudomolecule Gene Annotation | Genes | Soybean Cyst Nematode (tn10) | masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks | Masonbrink | orderedscngenepredictions.gff3.gz | View on JBrowse |
| TN10 H.glycines Pseudomolecule Functional Gene Annotation | Transcripts | Soybean Cyst Nematode (tn10) | Interpro, BLASTP NCBI NR, BLASTN NCBI nt, blastx, blastn, blastp to swissprot, Interproscan | Masonbrink | functionalannotations2.gff3.gz | View on JBrowse |
| TN10 H.glycines Pseudomolecule Transcript Sequences | Transcripts | Soybean Cyst Nematode (tn10) | cufflinks 2.2.1 | Masonbrink | orderedscngenepredictions_transcripts.fasta | |
| TN10 H.glycines Pseudomolecule Protein Sequences | Transcripts | Soybean Cyst Nematode (tn10) | cufflinks 2.2.1 | Masonbrink | orderedscngenepredictions_proteins.fasta | |
| Genes with transposon annotations | Genes | Soybean Cyst Nematode (tn10) | masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks | Masonbrink | orderedgeneswithtransposonannotations.gff3.gz | View on JBrowse |
| Repetitive Genes that overlap repeatmasker | Genes | Soybean Cyst Nematode (tn10) | masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks | Masonbrink | orderedrepeatsbyoverlap.gff3.gz | View on JBrowse |
| SRR6230586 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230586_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| Genes that lack expression | Genes | Soybean Cyst Nematode (tn10) | masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks | Masonbrink | orderednoexpressedmrnagene.gff3.gz | View on JBrowse |
| SRR6230579 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230579_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230587 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230587_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230583 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230583_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230585 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230585_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| Compatible RNAseq-- PA3 nematodes on susceptible host -- All Reps Merged | Gene expression | Soybean Cyst Nematode (tn10) | Hisat, Samtools, Bedtools | Rick Masonbrink | MergedRNACompatible_sorted.bw | View on JBrowse |
| Combined RNAseq | Gene expression | Soybean Cyst Nematode (tn10) | Hisat - Bedtools | Rick Masonbrink | MergedRNA.bw | View on JBrowse |
| SRR13711085 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | 1703FL-02-01_S1_L001_R1_001.fastqGene_sorted.bw | View on JBrowse | |
| SRR13711082 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | 1703FL-02-02_S2_L001_R1_001_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR13711081 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | 1703FL-02-03_S3_L001_R1_001_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR13711080 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | 1703FL-02-04_S4_L001_R1_001_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR13711084 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | 1703-TM101_S0_L003_R1_001_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR13711083 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | 1703-TM102_S0_L003_R1_001_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230580 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230580_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230581 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230581_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230582 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230582_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| SRR6230584 | Gene expression | Soybean Cyst Nematode (tn10) | Hisat2 Alignment | SRR6230584_1_val_1.fqGene_sorted.bw | View on JBrowse | |
| Incompatible RNAseq-- PA3 nematodes on resistant host (Forrest) -- All Reps Merged | Gene expression | Soybean Cyst Nematode (tn10) | Hisat, Samtools, Bedtools | Rick Masonbrink | MergedRNAIncompatible_sorted.bw | View on JBrowse |
| X12 Repeats | Genome structure | Soybean Cyst Nematode (X12v2) | tabix | Rick Masonbrink | OrderedX12repeatAnnotation.gff3.gz | View on JBrowse |
| 80 Effectors Aligned with Gmap | Genes | Soybean Cyst Nematode (X12v2) | Gmap | Rick Masonbrink | SortedOrderedJustGenesSCNgenome.effector.gff3.gz | View on JBrowse |
| PA3 J2 Gland RNA-SEQ -- All Reps Merged | Gene expression | Soybean Cyst Nematode (tn10) | Hisat, Samtools, Bedtools | Rick Masonbrink | MergedRNAPA3J2_sorted.bw | View on JBrowse |
| MM10 J2 Gland RNA-SEQ -- All Reps Merged | Gene expression | Soybean Cyst Nematode (tn10) | Hisat, Samtools, Bedtools | Rick Masonbrink | MergedRNAMM10J2A_sorted.bw | View on JBrowse |
| RNAseq of Preparasitic PA3 nematodes -- All Reps Merged | Gene expression | Soybean Cyst Nematode (tn10) | Hisat, Samtools, Bedtools | Rick Masonbrink | MergedRNAPP_sorted.bw | View on JBrowse |
| CDS of V2 Gene Models | Genes | Soybean Cyst Nematode (v2) | Fasta sequences of CDS V2 gene models | From genome assembly | gff2fasta.cds_.fasta | |
| Synteny to TN20 genome (ABLA00000000.1) synteny | Genome structure | Soybean Cyst Nematode (v2) | Braker gene prediction,opscan orthologue calling, iadhore synteny | Monsanto/JGI | jgisynteny.bed.gz | View on JBrowse |
| Meloidogyne and Globodera Synteny with H.glycines | Genome structure | Soybean Cyst Nematode (v2) | Opscan ortholog calling, iadhore syntenic fragment from multiple species merged with bedtools | H. glycines synteny with 3 Globodera and 2 Meloidogyne species | all.synteny_sorted.gff_.gz | View on JBrowse |
| NCBI ESTs | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.HglyEST.gff3.gz | View on JBrowse |
| TN19 Eggs Isoseq | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.SRR111798_31.gff3.gz | View on JBrowse |
| TN19 J2/J3 Isoseq | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.SRR111798_35.gff3.gz | View on JBrowse |
| PA3 J2/J3 Isoseq | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.SRR11179833.gff3.gz | View on JBrowse |
| PA3 Eggs Isoseq | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.SRR11179834.gff3.gz | View on JBrowse |
| PA3 J4/Adult Isoseq | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.SRR111798_32.gff3.gz | View on JBrowse |
| TN10 Draft Genes | Genes | Soybean Cyst Nematode (tn10) | Gmap | OrderedSCNgenome738Genes.gff3.gz | View on JBrowse | |
| TN19 J4/Adult Isoseq | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedSCNgenome.SRR1117983_0.gff3.gz | View on JBrowse |
| Predicted Proteome of X12v2 | Other | Soybean Cyst Nematode (X12v2) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | X12Proteins.fasta | |
| Gmap Alignment of X12 Genes | Genes | Soybean Cyst Nematode (v2) | Gmap | Rick Masonbrink | OrderedX12Transcripts2TN10DraftGenome.gff3.gz | View on JBrowse |
| Gmap Alignment of TN10 Pseudomolecule Transcripts | Genes | Soybean Cyst Nematode (v2) | Gmap | Rick Masonbrink | OrderedTN10PseudomoleculeTranscripts2TN10DraftGenome.gff3.gz | View on JBrowse |
| TN10 Draft Genome | Other | Soybean Cyst Nematode (v2) | Falcon | Rick Masonbrink | genome738sl.polished.mitofixed_YwRLEPj.fasta | |
| Transcriptome Gardner et al 2018 | Transcripts | Soybean Cyst Nematode (tn10) | Gmap | Rick Masonbrink | OrderedGardnerTranscriptome.gff3_RNbPpFb.gz | View on JBrowse |
| NCBI Nucleotide | Other | Soybean Cyst Nematode (tn10) | Minimap2 | Rick Masonbrink | OrderedNucleotide.gff3.gz | View on JBrowse |
| TN10 Draft Genes Aligned | Genes | Soybean Cyst Nematode (X12v2) | Gmap | OrderedX12Genome738Genes.gff3.gz | View on JBrowse | |
| J2_PH7 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | Jiang, Ye, et al 2023 | pH7_merged_sortedSense.bw | View on JBrowse |
| J2_NACL | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | NaCl_merged_sortedSense.bw | View on JBrowse | |
| J2_PH10 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | pH10_merged_sortedSense.bw | View on JBrowse | |
| J2_PH8.6 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | pH8.6_merged_sortedSense.bw | View on JBrowse | |
| J2_4.5 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | pH4.5_merged_sortedSense.bw | View on JBrowse | |
| J2_5.25 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | pH5.25_merged_sortedSense.bw | View on JBrowse | |
| QCSTJ6_PI88788 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | QCSTJ6_PI88788_merged_sortedSense.bw | View on JBrowse | |
| TN10 Pseudomolecule Genes Aligned | Genes | Soybean Cyst Nematode (X12v2) | Gmap | OrderedX12GenomeTN10pseudoGenes.gff3.gz | View on JBrowse | |
| QCSTJ5_Essex | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | QCSTJ5_Essex_merged_sortedSense.bw | View on JBrowse | |
| QCSTJ5_PI88788 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | QCSTJ5_PI88788_merged_sortedSense.bw | View on JBrowse | |
| QCSTJ6_PI88788 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | QCSTJ6_PI88788_merged_sortedSense_olG9EEv.bw | View on JBrowse | |
| QCSTJ6_Essex | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | QCSTJ6_Essex_merged_sortedSense.bw | View on JBrowse | |
| QCSTJ15_PI88788 | Gene expression | Soybean Cyst Nematode (tn10) | Minimap2 | QCSTJ15_PI88788_merged_sortedSense.bw | View on JBrowse | |
| Functional Gene Annotation TN22 | Genes | Soybean Cyst Nematode (TN22) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedTN22.gff3.gz | View on JBrowse |
| Functional Gene Annotation TN7 | Genes | Soybean Cyst Nematode (TN7) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedTN7.gff3.gz | View on JBrowse |
| Functional Gene Annotation TN8 | Genes | Soybean Cyst Nematode (TN8) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedTN8.gff3.gz | View on JBrowse |
| Functional Gene Annotation PA3 | Genes | Soybean Cyst Nematode (PA3) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedPA3.gff3.gz | View on JBrowse |
| Functional Gene Annotation OP50 | Genes | Soybean Cyst Nematode (OP50) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedOP50.gff3.gz | View on JBrowse |
| Functional Gene Annotation MM26 | Genes | Soybean Cyst Nematode (MM26) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedMM26.gff3.gz | View on JBrowse |
| Functional Gene Annotation TN20 | Genes | Soybean Cyst Nematode (TN20) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedTN20.gff3.gz | View on JBrowse |
| Functional Gene Annotation TN10v3 | Genes | Soybean Cyst Nematode (TN10v3) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedTN10.gff3.gz | View on JBrowse |
| All Expression Combined PA3 | Gene expression | Soybean Cyst Nematode (PA3) | STAR | Masonbrink:ISU GIF | 03_PA3_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| All Expression Combined MM26 | Gene expression | Soybean Cyst Nematode (MM26) | STAR | Masonbrink:ISU GIF | 01_MM26_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| All Expression Combined TN8 | Gene expression | Soybean Cyst Nematode (TN8) | STAR | Masonbrink:ISU GIF | 07_TN8_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| All Expression Combined OP50 | Gene expression | Soybean Cyst Nematode (OP50) | STAR | Masonbrink:ISU GIF | 02_OP50_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| All Expression Combined TN7 | Gene expression | Soybean Cyst Nematode (TN7) | STAR | Masonbrink:ISU GIF | 06_TN7_HQAllMergedShortRNA_sorted_rOJOe4G.bw | View on JBrowse |
| All Expression Combined TN10v3 | Gene expression | Soybean Cyst Nematode (TN10v3) | STAR | Masonbrink:ISU GIF | HQMergedLongDistRNASplices_sorted.bw | View on JBrowse |
| Functional Gene Annotation X12 | Genes | Soybean Cyst Nematode (X12v2) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OrderedReformattedX12.gff3.gz | View on JBrowse |
| All Expression Combined TN20 | Gene expression | Soybean Cyst Nematode (TN20) | STAR | Masonbrink:ISU GIF | 04_TN20_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| All Expression Combined TN22 | Gene expression | Soybean Cyst Nematode (TN22) | STAR | Masonbrink:ISU GIF | 05_TN22_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| All Expression Combined X12 | Gene expression | Soybean Cyst Nematode (X12v2) | STAR | Masonbrink:ISU GIF | 08_X12_HQAllMergedShortRNA_sorted.bw | View on JBrowse |
| RepeatModeler X12 (9 Genome models) | Genome structure | Soybean Cyst Nematode (X12v2) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedSoftmaskedX12.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler TN22 (9 Genome models) | Genome structure | Soybean Cyst Nematode (TN22) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedTN22.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler TN20 (9 Genome models) | Genome structure | Soybean Cyst Nematode (TN20) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedTN20.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler TN8 (9 Genome models) | Genome structure | Soybean Cyst Nematode (TN8) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedTN8.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler TN7 (9 Genome models) | Genome structure | Soybean Cyst Nematode (TN7) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedTN7.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler OP50 (9 Genome models) | Genome structure | Soybean Cyst Nematode (OP50) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedOP50.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler MM26 (9 Genome models) | Genome structure | Soybean Cyst Nematode (MM26) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedSoftmaskedMM26.fasta.out.gff.gz | View on JBrowse |
| RepeatModeler PA3 (9 Genome models) | Genome structure | Soybean Cyst Nematode (PA3) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedSoftmaskedPA3.fasta.out.gff.gz | View on JBrowse |
| Published Effectors TN8 | Genes | Soybean Cyst Nematode (TN8) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsTN8.gff3.gz | View on JBrowse |
| Published Effectors TN22 | Genes | Soybean Cyst Nematode (TN22) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsTN22.gff3.gz | View on JBrowse |
| Published Effectors TN20 | Genes | Soybean Cyst Nematode (TN20) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsTN20.gff3.gz | View on JBrowse |
| Published Effectors TN7 | Genes | Soybean Cyst Nematode (TN7) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsTN7.gff3.gz | View on JBrowse |
| Published Effectors PA3 | Genes | Soybean Cyst Nematode (PA3) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsSoftmaskedPA3.gff3.gz | View on JBrowse |
| Published Effectors OP50 | Genes | Soybean Cyst Nematode (OP50) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsOP50.gff3.gz | View on JBrowse |
| Published Effectors TN10v3 | Genes | Soybean Cyst Nematode (TN10v3) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsTN10Genome.gff3.gz | View on JBrowse |
| RepeatModeler TN10v3 (9 Genome models) | Genome structure | Soybean Cyst Nematode (TN10v3) | RepeatModeler and RepeatMasker | Masonbrink:ISU GIF | RMPLURALOrderedSortedTN10Genome.fasta.out.gff.gz | View on JBrowse |
| Published Effectors MM26 | Genes | Soybean Cyst Nematode (MM26) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsSoftmaskedMM26.gff3.gz | View on JBrowse |
| Published Effectors X12 | Genes | Soybean Cyst Nematode (X12v2) | GMAP | Masonbrink:ISU GIF | OrderedEffectorsSoftmaskedX12.gff3.gz | View on JBrowse |
| All Expression Combined Nanopore cDNA TN22 | Gene expression | Soybean Cyst Nematode (TN22) | Minimap2 | Masonbrink:ISU GIF | 05_TN22_HQAllNanopore_TN22_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA X12 | Gene expression | Soybean Cyst Nematode (X12v2) | Minimap2 | Masonbrink:ISU GIF | 08_X12_HQAllNanopore_SoftmaskedX12_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA TN20 | Gene expression | Soybean Cyst Nematode (TN20) | Minimap2 | Masonbrink:ISU GIF | 04_TN20_HQAllNanopore_TN20_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA TN8 | Gene expression | Soybean Cyst Nematode (TN8) | Minimap2 | Masonbrink:ISU GIF | 07_TN8_HQAllNanopore_TN8_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA TN7 | Gene expression | Soybean Cyst Nematode (TN7) | Minimap2 | Masonbrink:ISU GIF | 06_TN7_HQAllNanopore_TN7_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA PA3 | Gene expression | Soybean Cyst Nematode (PA3) | Minimap2 | Masonbrink:ISU GIF | 03_PA3_HQAllNanopore_SoftmaskedPA3_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA OP50 | Gene expression | Soybean Cyst Nematode (OP50) | Minimap2 | Masonbrink:ISU GIF | 02_OP50_HQAllNanopore_OP50_minimap2_sorted.bw | View on JBrowse |
| All Expression Combined Nanopore cDNA MM26 | Gene expression | Soybean Cyst Nematode (MM26) | Minimap2 | Masonbrink:ISU GIF | 01_MM26_HQAllNanopore_SoftmaskedMM26_minimap2_sorted.bw | View on JBrowse |
| EDTA Repeats TN10v3 | Genome structure | Soybean Cyst Nematode (TN10v3) | EDTA | SortedFormattedTN10Genome.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse | |
| EDTA Repeats X12 | Genome structure | Soybean Cyst Nematode (X12v2) | EDTA | Masonbrink:ISU GIF | SortedFormattedSoftmaskedX12.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats TN22 | Genome structure | Soybean Cyst Nematode (TN22) | EDTA | Masonbrink:ISU GIF | SortedFormattedTN22.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats TN20 | Genome structure | Soybean Cyst Nematode (TN20) | EDTA | Masonbrink:ISU GIF | SortedFormattedTN20.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats TN8 | Genome structure | Soybean Cyst Nematode (TN8) | EDTA | Masonbrink:ISU GIF | SortedFormattedTN8.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats TN7 | Genome structure | Soybean Cyst Nematode (TN7) | EDTA | Masonbrink:ISU GIF | SortedFormattedTN7.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats PA3 | Genome structure | Soybean Cyst Nematode (PA3) | EDTA | Masonbrink:ISU GIF | SortedFormattedSoftmaskedPA3.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats OP50 | Genome structure | Soybean Cyst Nematode (OP50) | EDTA | Masonbrink:ISU GIF | SortedFormattedOP50.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| EDTA Repeats MM26 | Genome structure | Soybean Cyst Nematode (MM26) | EDTA | Masonbrink:ISU GIF | SortedFormattedSoftmaskedMM26.fasta.mod.EDTA.intact.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA TN10v3 | Transcripts | Soybean Cyst Nematode (TN10v3) | Stringtie | Masonbrink:ISU GIF | OrderedStringtieMixTN10ProposedCoding.gff3.gz | View on JBrowse |
| All Expression Combined Nanopore cDNA TN10v3 | Gene expression | Soybean Cyst Nematode (TN10v3) | Minimap2 | Masonbrink:ISU GIF | 10_TN10_Polish_HQAllNanopore_RNAPolishTN10Genomeq40_minimap3_sorted.bw | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA TN20 | Transcripts | Soybean Cyst Nematode (TN20) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixTN20ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA TN22 | Transcripts | Soybean Cyst Nematode (TN22) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixTN22ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA X12 | Transcripts | Soybean Cyst Nematode (X12v2) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixX12ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA PA3 | Transcripts | Soybean Cyst Nematode (PA3) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixPA3ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA TN7 | Transcripts | Soybean Cyst Nematode (TN7) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixTN7ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA TN8 | Transcripts | Soybean Cyst Nematode (TN8) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixTN8ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA OP50 | Transcripts | Soybean Cyst Nematode (OP50) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixOP50ProposedCoding.gff3.gz | View on JBrowse |
| Stringtie Assembly of RNAseq and Nanopore cDNA MM26 | Transcripts | Soybean Cyst Nematode (MM26) | Stringtie | Masonbrink:ISU GIF | OrderedSortedStringtieMixMM26ProposedCoding.gff3.gz | View on JBrowse |
| Genome Assembly PA3 | Other | Soybean Cyst Nematode (PA3) | More to come | SoftmaskedPA3.fasta | ||
| Genome Assembly TN7 | Other | Soybean Cyst Nematode (TN7) | More to come | Masonbrink:ISU GIF | TN7.fasta | |
| Genome Assembly TN8 | Other | Soybean Cyst Nematode (TN8) | More to come | Masonbrink:ISU GIF | TN8.fasta | |
| Genome Assembly TN20 | Other | Soybean Cyst Nematode (TN20) | More to come | Masonbrink:ISU GIF | TN20.fasta | |
| Genome Assembly TN22 | Other | Soybean Cyst Nematode (TN22) | More to come | Masonbrink:ISU GIF | TN22.fasta | |
| Genome Assembly X12 | Other | Soybean Cyst Nematode (X12v2) | FALCON | Masonbrink:ISU GIF | SoftmaskedX12.fasta | |
| Genome Assembly MM26 | Other | Soybean Cyst Nematode (MM26) | More to come | Masonbrink:ISU GIF | SoftmaskedMM26.fasta | |
| Genome Assembly OP50 | Other | Soybean Cyst Nematode (OP50) | More to come | Masonbrink:ISU GIF | OP50.fasta | |
| Genome Assembly TN10v3 | Other | Soybean Cyst Nematode (TN10v3) | FLYE | Masonbrink:ISU GIF | TN10Genome.fasta | |
| Predicted Proteome of OP50 | Other | Soybean Cyst Nematode (OP50) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | OP50Proteins.fasta | |
| Predicted Proteome of PA3 | Other | Soybean Cyst Nematode (PA3) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | PA3Proteins.fasta | |
| Predicted Proteome of TN7 | Other | Soybean Cyst Nematode (TN7) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | TN7_hwPcOiu.fasta | |
| Predicted Proteome of TN8 | Other | Soybean Cyst Nematode (TN8) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | TN8Proteins.fasta | |
| Predicted Proteome of TN10v3 | Other | Soybean Cyst Nematode (TN10v3) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | TN10Proteins.fasta | |
| Predicted Proteome of TN20 | Other | Soybean Cyst Nematode (TN20) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | TN20Proteins.fasta | |
| Predicted Proteome of TN22 | Other | Soybean Cyst Nematode (TN22) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | TN22Proteins.fasta | |
| Predicted Proteome of MM26 | Other | Soybean Cyst Nematode (MM26) | Braker/Stringtie/Mikado | Masonbrink:ISU GIF | MM26Proteins.fasta |