Indices builder from GBOL RDF (TTL)
Version 1

Work-in-progress

Workflow to build different indices for different tools from a genome and transcriptome.

This workflow expects an (annotated) genome in GBOL ttl format.

Steps:

  • SAPP: rdf2gtf (genome fasta)

  • SAPP: rdf2fasta (transcripts fasta)

  • STAR index (Optional for Eukaryotic origin)

  • bowtie2 index

  • kallisto index

Inputs

ID Name Description Type
threads number of threads number of threads to use for computational processes int?
memory maximum memory usage in megabytes maximum memory usage in megabytes int?
inputFile turtle file Annotated genome in GBOL turtle file (.ttl) format File
run_star Run STAR create STAR index for genome if true. (For genomes with exons) boolean
genomeSAindexNbases STAR parameter For small genomes, the parameter --genomeSAindexNbases must be scaled down. int?

Steps

ID Name Description
rdf2gtf RDF to GTF Convert input RDF (turtle) file to GTF file
rdf2fasta RDF to Fasta Convert input RDF (turtle) file to Genome fasta file.
STAR STAR index Creates STAR index with genome fasta and GTF file
bowtie2 bowtie2 index Creates bowtie2 index with genome fasta
kallisto kallisto index Creates kallisto index with transcripts fasta file

Outputs

ID Name Description Type
STAR STAR STAR index folder Directory
bowtie2 bowtie2 bowtie2 index folder Directory
kallisto kallisto kallisto index folder Directory
genomefasta Genome fasta Genome fasta file File
gtf GTF Genes in GTF format File
transcripts Transcripts Transcripts fasta file File
proteins Proteins Proteins fasta file File
help Creators and Submitter
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Views: 212   Downloads: 13

Created: 23rd Nov 2020 at 16:22

Last used: 16th Apr 2021 at 16:30

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Version History

Version 1 Created 23rd Nov 2020 at 16:22 by Bart Nijsse

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