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Name Category Organism Program, Pipeline Name or Method Name Source Name Download link
Genes that lack expression -- protein fasta sequences Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data noexpressedmrnagene_protein.fasta
Genes that lack expression -- transcript fasta sequences Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data noexpressedmrnagene_transcript.fasta
Genes that lack expression Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data orderednoexpressedmrnagene.gff3.gz View on JBrowse
Repetitive Genes that overlap repeatmasker protein fasta Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data repeatsbyoverlap_protein.fasta
Repetitive Genes that overlap repeatmasker transcript fasta Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data repeatsbyoverlap_transcript.fasta
Repetitive Genes that overlap repeatmasker Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data orderedrepeatsbyoverlap.gff3.gz View on JBrowse
Genes with transposon annotations protein fasta Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) cufflinks 2.2.1 Masonbrink Binary Data geneswithtransposonannotations_protein.fasta
Genes with transposon annotations transcripts fasta Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) cufflinks 2.2.1 Masonbrink Binary Data geneswithtransposonannotations_transcript.fasta
Genes with transposon annotations Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data orderedgeneswithtransposonannotations.gff3.gz View on JBrowse
TN10 H.glycines Pseudomolecule Protein Sequences Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) cufflinks 2.2.1 Masonbrink Binary Data orderedscngenepredictions_proteins.fasta
TN10 H.glycines Pseudomolecule Transcript Sequences Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) cufflinks 2.2.1 Masonbrink Binary Data orderedscngenepredictions_transcripts.fasta
TN10 H.glycines Pseudomolecule Functional Gene Annotation Transcripts Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Interpro, BLASTP NCBI NR, BLASTN NCBI nt, blastx, blastn, blastp to swissprot, Interproscan Masonbrink Binary Data functionalannotations2.gff3.gz View on JBrowse
TN10 H.glycines Pseudomolecule Gene Annotation Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data orderedscngenepredictions.gff3.gz View on JBrowse
TN10 H.glycines Pseudomolecule Assembly Sequence Genome structure Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Falcon, Falcon unzip, Dovetail genomics, Sspace, Juicer/3D-DNA, pilon Masonbrink Binary Data scngenome.fasta
TN10 SNPS/INDELS Molecular markers (QTL) Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Freebayes 1.1.0, bcftools 1.10.2 filter Masonbrink Binary Data sortscngenome.tn10sm.vcf.gz View on JBrowse
SVIM TN10 Pacbio Structural Variants Genome structure Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) minimap2 mapping and SVIM Masonbrink Binary Data svimvariants.vcf.gz View on JBrowse
Tandem Repeats Finder Genome structure Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Tandem Repeats Finder Masonbrink Binary Data sortedtrf.bed.gz View on JBrowse
Ribosomal Genes Genome structure Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) BLAST of nematode ribosomal genes from NCBI Masonbrink Binary Data ribocoordsfix.bed.gz View on JBrowse
EDTA Annotated Transposons Genome structure Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) EDTA Extensive Denovo Transposon Annotator Masonbrink Binary Data edtatransposons1.gff3.gz View on JBrowse
NCRNAs Mikado Prediction Noncoding RNAs Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) mikado prediction of NCRNAs Masonbrink Binary Data ncrnas.gff3.gz View on JBrowse
Repeatmasker Genome structure Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Repeatmodeler Prediction, Repeatmasker Annotation Masonbrink Binary Data repeatmasker.gff_.gz View on JBrowse
Genomethreader Alignment of X12 Annotation Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Genomethreader of Published Annotation Liam et al Gene Models, Masonbrink alignment Binary Data x12genomethreader.gff_.gz View on JBrowse
80 Published Effectors Nucleotide Alignment (GMAP) Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Gmap Alignment of 80 Published Effectors Nucleotide alignment with Gmap, default parameters Binary Data gmapeffectors.gff_.gz View on JBrowse
Published Effectors via protein-protein alignment Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) Diamond Alignment of 80 Published Effectors Protein protein alignment with Diamond, default parameters Binary Data diamondeffectors.gff3.gz View on JBrowse
Input Transcriptome Assemblies to Final Prediction Genes Heterodera glycines tn10 (Soybean Cyst Nematode (tn10)) masked Braker2, Class2, unmasked Braker2, Stringtie, RNASpades, Portcullis, Mikado, Cufflinks Masonbrink Binary Data orderedmergingtestscn.gff3.resortfixed.gff_.gz View on JBrowse
Fasta sequences of the 80 published effector genes Transcripts Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Collected from literature Baum/Severin Labs Binary Data effector.fasta
Transcripts of genes producing secreted proteins Transcripts Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Braker genes, SignalP and Tmhmm Baum/Severin Labs Binary Data secretedtranscripts.fasta
24H attraction SCN exposed to roots -- SRR5447113 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447113 , Chinese Academy of Sciences Binary Data srr5447113_1.fastq_sorted.bw View on JBrowse
Alignments of genes producing secreted proteins Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Braker genes, SignalP Genes with N terminal secretion signals, and lacking transmembrane domains Binary Data reworkedfunctionalaugustussecreted_sorted.gff_.gz View on JBrowse
Trinity Transcripts form Gardner et al 2017 Transcripts Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Gmap alignment NCBI Bioproject PRJNA415980 Binary Data scngenome.gfzz01.1_sorted.gff_.gz View on JBrowse
3H attraction SCN exposed to roots -- SRR5447116 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447116_1 , Chinese Academy of Sciences Binary Data srr5447116_1.fastq_sorted.bw View on JBrowse
3H attraction SCN exposed to roots -- SRR5447111 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447111_1 , Chinese Academy of Sciences Binary Data srr5447111_1.fastq_sorted.bw View on JBrowse
3H control SCN exposed to roots -- SRR5447109 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447109_1 , Chinese Academy of Sciences Binary Data srr5447109_1.fastq_sorted.bw View on JBrowse
24H control SCN exposed to roots -- SRR5447110 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447110 , Chinese Academy of Sciences Binary Data srr5447110_1.fastq_sorted.bw View on JBrowse
24H attraction SCN exposed to roots -- SRR5447112 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447112 , Chinese Academy of Sciences Binary Data srr5447112_1.fastq_sorted.bw View on JBrowse
24H control SCN exposed to roots -- SRR5447114 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447114 , Chinese Academy of Sciences Binary Data srr5447114_1.fastq_sorted.bw View on JBrowse
24H control SCN exposed to roots -- SRR5447115 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447115 , Chinese Academy of Sciences Binary Data srr5447115_1.fastq_sorted.bw View on JBrowse
3H attraction SCN exposed to roots -- SRR5447117 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447117 , Chinese Academy of Sciences Binary Data srr5447117_1.fastq_sorted.bw View on JBrowse
3H control SCN exposed to roots -- SRR5447118 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447118 , Chinese Academy of Sciences Binary Data srr5447118_1.fastq_sorted.bw View on JBrowse
3H control SCN exposed to roots -- SRR5447119 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447119 , Chinese Academy of Sciences Binary Data srr5447119_1.fastq_sorted.bw View on JBrowse
24H attraction SCN exposed to roots -- SRR5447108 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trim_galore, Hisat2, Samtools, Bedtools, BedgraphToBigwig SRR5447108 , Chinese Academy of Sciences Binary Data srr5447108_1.fastq_sorted.bw View on JBrowse
Globodera Ellingtonae Gene Predictions Related species Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Hisat2, Braker Baum/Severin Labs, GCA_001723225.1, SRR3162514 Binary Data globoderaellingtonaegenepredictions.gff_.gz
Annotated Braker Gene Models IPRSCAN Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Interproscan, Swissprot, Uniref Baum/Severin Labs Binary Data annotatedcorrectlyaugustus_sorted77.gff_.gz View on JBrowse
Predicted Proteins from V2 Gene Models Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) braker gene prediction, gff2fasta From genome assembly Binary Data finalaugustus.pep_.fasta
Annotated Gene Models Heterodera Glycines (updated v2) Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Ortholog based Manual Annotations Baum/Severin Labs Binary Data reworkedfunctionalaugustus_sorted_gff0.gz View on JBrowse
Repeat Explorer of TN20 Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) RepeatExplorer2, GMAP SRR3924425 Binary Data nononsensehashes_sorted.gff_.gz View on JBrowse
CDS of V2 Gene Models Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Fasta sequences of CDS V2 gene models From genome assembly Binary Data gff2fasta.cds_.fasta
H.glycines genome assembly (ABLA00000000.1) synteny Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Braker gene prediction,opscan orthologue calling, iadhore synteny Monsanto/JGI Binary Data jgisynteny.bed.gz View on JBrowse
Pre-parasitic J2 (PA3) Biorep 2 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig Pre-parasitic J2 (PA3) Biorep 2 Binary Data sortedppj2_pa3_atcacg.bam.bw View on JBrowse
Parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 2 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 Binary Data sortedpj2_s63_ttaggc.bam.bw View on JBrowse
Parasitic J2 (PA3) Forrest (Resistant Soybean) Biorep 1 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig parasitic J2 (PA3) Race 3 Forrest (Resistant soybean cultivar) Biorep 1 Binary Data sortedpj2_race3_forrest.bam.bw View on JBrowse
Pre-parasitic J2 (PA3) Biorep 1 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig Pre-parasitic J2 (PA3) Biorep 1 Binary Data sortedppj2_pa3_tagctt.bam.bw View on JBrowse
parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig parasitic J2 (PA3) EXF63 (Susceptible soybean cultivar) Biorep 1 Binary Data sortedpj2_s63_tgacca.bam.bw View on JBrowse
Parasitic J2 (PA3) Forrest (Resistant Soybean) Biorep 2 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) hisat2,samtools,bedtools genomcov,bioawk, bedGraphToBigWig parasitic J2 (PA3) Race 3 Forrest (Resistant soybean cultivar) Biorep 2 Binary Data sortedpj2_race_3.bw View on JBrowse
Mitochondrial Genes Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) mitos webserver alternative flatworm From genome assembly Binary Data mitochondria.gff3.gz View on JBrowse
Genome version 1 with 738 scaffolds Genome structure Heterodera glycines (Soybean Cyst Nematode (v1)) Asssembly - Falcon of transcript mapping preassembled subreads TN10 Binary Data genome738sl.polished.mitofixed.fasta
W82_TN19_J2/J3 Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap IDX6 Isoseq Baum/Severin Binary Data sortedidx6_isoforms_present.bed.gz View on JBrowse
W82_TN19_J4/Adult Isoseq reads Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap IDX5 Isoseq Baum/Severin Binary Data sortedidx5_isoforms_present.bed.gz View on JBrowse
W82_TN19_Eggs Isoseq reads Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap IDX4 Isoseq Baum/Severin Binary Data sortedidx4_isoforms_present.bed.gz View on JBrowse
W82_PA3_J4/Adult Isoseq reads Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap IDX3 Isoseq Baum/Severin Binary Data sortedidx3_isoforms_present.bed.gz View on JBrowse
W82_PA3_J2/J3 Isoseq reads Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap IDX2 Isoseq Baum/Severin Binary Data sortedidx2_isoforms_present.bed.gz View on JBrowse
W82_PA3_Eggs Isoseq reads Gene expression Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap IDX1 Isoseq Baum/Severin Binary Data sortedidx1_isoforms_present.bed.gz View on JBrowse
Camtech Raw Pacbio RS II subreads Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Blasr mapping of raw Pacbio subreads Raw Pacbio subreads (TN10) Binary Data subreads2genome.gff_.gz View on JBrowse
Circular Consensus Pacbio RS II subreads (CCS Reads) Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Blasr mapping of CCS Pacbio reads circular consensus reads assembled with smrtanalysis_2.3.0.140936. Binary Data ccs2genome.gff_.gz View on JBrowse
Falcon Assembled Pacbio RS II subreads (pReads) Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Blasr mapping of Pacbio preads to H.glycines genome Pacbio pread mapping to genome Binary Data preads2genomegff.gz View on JBrowse
Alignment of 80 published known effector genes (gff3) Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Gmap alignment with default parameters 80 Known effectors Thomas Baum Lab Binary Data test2.gz View on JBrowse
SNPs across 15 populations of H.glycines Molecular markers (QTL) Heterodera glycines v2 (Soybean Cyst Nematode (v2)) GATK Best Practices: BWA-mem, Picard, GATK SNPs called from 15 populations of H. glycines Binary Data sortedrenamed.combined_variants.vcf.gz View on JBrowse
Genes with promoters containing DOG-box motifs Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) MEME to find Dog Box, BLAST to align GS-like effectors H.glycines Dog-box genes Binary Data dorsal-likegenessorted.bed.gz View on JBrowse
Helitrons Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Helitron Scanner HelitronScanner default on H. glycines genome Binary Data helitronnamedsorted.bed.gz View on JBrowse
80 Effector MEME->FIMO motifs Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) MEME of 80 effector proteins, Genes with protein motifs found with FIMO Effector Motifs from the 80 known motifs Binary Data fimogenessorted.bed.gz View on JBrowse
DNA Transposons Genome structure Heterodera glycines v2 (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 Binary Data supportedirfmergeclassifiedscnbasesorted.bed.gz View on JBrowse
LTR Retroelements Genome structure Heterodera glycines v2 (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 Binary Data ltrretroelementsclassifiedcut_sorted.gff_.gz View on JBrowse
Meloidogyne and Globodera Synteny with H.glycines Genome structure Heterodera glycines v2 (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 Binary Data all.synteny_sorted.gff_.gz View on JBrowse
Globodera pallida Synteny with H.glycines Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Opscan ortholog calling, iadhore syntenic fragment H. glycines synteny with G. pallida genome (2017) Binary Data pallida_syntenic_ribbons_sorted_txt_gff_sorted.gff_.gz View on JBrowse
Meloidogyne hapla Synteny with H.glycines Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Opscan ortholog calling, iadhore syntenic fragment H. glycines synteny with M. hapla genome (2008) Binary Data hapla_syntenic_ribbons_txt_gff_sorted.gff_.gz View on JBrowse
Globodera ellingtonae Synteny with H.glycines Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Braker,Opscan ortholog calling, iadhore syntenic fragment H. glycines synteny with G. ellingtonae genome (2017) Binary Data ellingtonae_syntenic_ribbons_txt_gff_sorted.gff_.gz View on JBrowse
Meloidogyne Incognita Syntenic Regions Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Opscan ortholog calling, iadhore syntenic fragment H. glycines synteny with M. incognita genome (2016) Binary Data incognita_syntenic_ribbons_txt_gff_sorted.gff_.gz View on JBrowse
High Confidence Horizontal Gene Transfers Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) H. glycines high confidence HGT H. glycines high confidence HGT Binary Data highconfhgtsorted.bed.gz View on JBrowse
Tandem Duplications Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Red Tandem used one scaffold at a time H. glycines genomic tandem duplications Binary Data redtandemalljbrowsesort.bed.gz View on JBrowse
Globodera rostochiensis Synteny with H.glycines Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Opscan ortholog calling, iadhore syntenic fragment H. glycines synteny with G. rostochiensis genome (2016) Binary Data rostochiensis_syntenic_ribbons_txt_gfffixed_sorted.gff_.gz View on JBrowse
NCBI EST Database Entries Transcripts Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Gmap NCBI EST entries for H. glycines Binary Data ests_mapped_sorted_gff_sorted_sorted.gff_.gz View on JBrowse
NCBI Nucleotide Database Entries Genes Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Gmap NCBI Nucleotide entries for H. glycines Binary Data nucleotide_mapped_sorted_sorted.gff_.gz View on JBrowse
Consensus Isoseq Transcriptome from PA3 and TN19 Transcripts Heterodera glycines v2 (Soybean Cyst Nematode (v2)) SmartPortal, Gmap H.glycines Isoseq Consensus isoforms Binary Data genome738sl.polished.consensus_isoforms_sorted.gff_.gz View on JBrowse
PA3 Transcriptome on susceptible and resistant soybean Transcripts Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Trinity transcriptome with Gmap alignment PA3 H. glycines transcriptome. Grown on susceptible and resistant soybean cultivars Binary Data nematode_transcripts_trinity.fasta_sorted_sorted.gff_.gz View on JBrowse
RepeatModeler Repeats Genome structure Heterodera glycines v2 (Soybean Cyst Nematode (v2)) Standard repeatmodeler and repeatmasker pipeline H. glycines Genome Repeatmodeler Repeats Binary Data genome738sl.polished.mitofixed.fa_.out_sorted.gff_.gz View on JBrowse
Tandem Duplicates Genome structure Heterodera glycines (Soybean Cyst Nematode (v1)) RedTandem ISU Genome Informatics Facility and Thomas Baum Lab Binary Data test_sorted_formatted_gff.gz View on JBrowse
Genome Annotations (Version 1) Merged gene models Genes Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP,Tabix ISU Genome Informatics Facility and Thomas Baum Lab Binary Data annotatedcorrectlyaugustus_sorted.gff_.gz View on JBrowse
Mitos Alternative Flatworm Genes Heterodera glycines (Soybean Cyst Nematode (v1)) MITOS webserver code 14 alternative flatworm ISU Genome Informatics Facility and Thomas Baum Lab Binary Data altflatwormcode.fixed_sorted._formatted.gff_.gz View on JBrowse
Mitochondria Gibson et al Genes Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP of Gibson et al genes. ISU Genome Informatics Facility and Thomas Baum Lab Binary Data gibson.redone_sorted_formatted.gff_.gz View on JBrowse
Mitchum Trinity Transcripts All 2-17-17 Transcripts Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP,Tabix one population, multiple life stages, Melissa Mitchum Binary Data nematode_transcripts_trinity.fasta_sorted_formatted.gff_.gz View on JBrowse
NCBI_Nucleotide_All Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP,Tabix ISU Genome Informatics Facility and Thomas Baum Lab Binary Data nucleotide_mapped_sorted_formatted.gff_.gz View on JBrowse
ISOseq read mapping All Transcripts Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP,Tabix ISU Genome Informatics Facility and Thomas Baum Lab Binary Data isoseq_738_sorted_formatted.gff_.gz View on JBrowse
NCBI_ESTs_All Transcripts Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP,Tabix ISU Genome Informatics Facility and Thomas Baum Lab Binary Data ests_mapped_sorted_gff_sorted_formatted.gff_.gz View on JBrowse
Known Effectors 02-10 Genes Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP ISU Genome Informatics Facility and Thomas Baum Lab Binary Data effector.gmapped.gff3.gz View on JBrowse
RepeatExplorer Genome structure Heterodera glycines (Soybean Cyst Nematode (v1)) GMAP ISU Genome Informatics Facility and Thomas Baum Lab Binary Data repeatexplorer.gff3.gz View on JBrowse
Gene Predictions No Masking Genes Heterodera glycines (Soybean Cyst Nematode (v1)) No repeatmasking, braker Thomas Baum Lab/Iowa State University Binary Data sorted_unmasked_738mitofixed.gff3.gz View on JBrowse
pJ2_s63_TGACCA Gene expression Heterodera glycines (Soybean Cyst Nematode (v1)) trimmomatic, hisat2 one population, multiple life stages, Melissa Mitchum Binary Data pj2_s63_tgacca_l001_r1_001_fastq_gz_paired_fq_rnaseq_sorted.bam View on JBrowse
Synteny Meloidogyne incognita Related species Heterodera glycines (Soybean Cyst Nematode (v1)) opscan,iadhore ISU Genome Informatics Facility Binary Data incognita_syntenic_ribbons_txt_gff.gz View on JBrowse
Synteny Meloidogyne hapla Related species Heterodera glycines (Soybean Cyst Nematode (v1)) opscan,iadhore ISU Genome Informatics Facility Binary Data hapla_syntenic_ribbons_txt_gff.gz View on JBrowse
Synteny Globodera ellingtonae Related species Heterodera glycines (Soybean Cyst Nematode (v1)) opscan,iadhore ISU Genome Informatics Facility Binary Data ellingtonae_syntenic_ribbons_txt_gff.gz View on JBrowse

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