Genome structure

TN10 H.glycines Pseudomolecule Assembly Sequence

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
Falcon, Falcon unzip, Dovetail genomics, Sspace, Juicer/3D-DNA, pilon
Program, Pipeline or Method version: 
N/A
Source Name: 
Masonbrink
Time Executed: 
03/12/2021
Materials & Methods (Description and/or Program Settings): 
https://www.authorea.com/doi/full/10.22541/au.161538368.83631935/v1 Until accepted for publication, cite as Rick Masonbrink, Tom Maier, Matthew Hudson, et al. A chromosomal assembly of the soybean cyst nematode genome. Authorea. March 10, 2021.
Category: 
Default Track?: 

Ribosomal Genes

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
BLAST of nematode ribosomal genes from NCBI
Program, Pipeline or Method version: 
blast-plus/2.9.0-py3-iv736hj
Source Name: 
Masonbrink
Time Executed: 
12/11/2020
Category: 
Default Track?: 

EDTA Annotated Transposons

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
EDTA Extensive Denovo Transposon Annotator
Program, Pipeline or Method version: 
(EDTA) v1.7.3
Source Name: 
Masonbrink
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
./EDTA.pl --genome SCNgenome.fasta --threads 16 --overwrite 1 --anno 1 --sensitive 1
Category: 
Default Track?: 

Repeatmasker

Organism: 
Heterodera glycines tn10 (Soybean Cyst Nematode (tn10))
Program, Pipeline Name or Method Name: 
Repeatmodeler Prediction, Repeatmasker Annotation
Program, Pipeline or Method version: 
repeatmodeler/1.0.11, repeatmasker/4.0.7
Source Name: 
Masonbrink
Time Executed: 
12/11/2020
Materials & Methods (Description and/or Program Settings): 
repeatmodeler/1.0.11-openmpi3-5v7auyo repeatmasker/4.0.7
Category: 
Default Track?: 

M6A Basemods PacBio

Organism: 
Heterodera glycines tn10 private (Soybean Cyst Nematode (tn10) private)
Program, Pipeline Name or Method Name: 
Smrttools
Program, Pipeline or Method version: 
smrttools 4.0
Source Name: 
Masonbrink from published TN10 Pacbio
Time Executed: 
12/10/2020
Materials & Methods (Description and/or Program Settings): 
ipdSummary subreadsPBbam.bam --identify M6A --reference SCNgenome.fasta --gff basemodsIdentify.gff
Category: 
Default Track?: 

Repeat Explorer of TN20

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
RepeatExplorer2, GMAP
Program, Pipeline or Method version: 
RepeatExplorer2, GMAP
Source Name: 
SRR3924425
Time Executed: 
10/26/2018
Materials & Methods (Description and/or Program Settings): 
Paired end DNA sequencing was downloaded from the SRA database (SRR3924425). Reads were trimmed, formatted, and submitted to Repeatexplorer2. GMAP was then used to map clustered repeats to the genome.
Category: 

H.glycines genome assembly (ABLA00000000.1) synteny

Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
Braker gene prediction,opscan orthologue calling, iadhore synteny
Program, Pipeline or Method version: 
braker1.9, Opscan 0.1, iAdHoRe 3.0.01
Source Name: 
Monsanto/JGI
Time Executed: 
06/01/2018
Materials & Methods (Description and/or Program Settings): 
Genes were called on the JGI assembly using braker and RNA-seq data. Orthologs were called using opscan, and synteny was inferred with iadhore. Submitter: Monsanto Assembly level: Scaffold Assembly: GCA_000150805.1 HG2 scaffolds: 34,708 contigs: 45,541 N50: 2,067 L50: 11,640 BioProjects: PRJNA56061, PRJNA28939 Whole Genome Shotgun (WGS): INSDC: ABLA00000000.1 Statistics: total length (Mb): 81.908 GC%: 37.5
Category: 

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