Indices builder from GBOL RDF (TTL) Version 1
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Download RO CrateWorkflow 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 |
|
| memory | maximum memory usage in megabytes | maximum memory usage in megabytes |
|
| inputFile | turtle file | Annotated genome in GBOL turtle file (.ttl) format |
|
| run_star | Run STAR | create STAR index for genome if true. (For genomes with exons) |
|
| genomeSAindexNbases | STAR parameter | For small genomes, the parameter --genomeSAindexNbases must be scaled down. |
|
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 |
|
| bowtie2 | bowtie2 | bowtie2 index folder |
|
| kallisto | kallisto | kallisto index folder |
|
| genomefasta | Genome fasta | Genome fasta file |
|
| gtf | GTF | Genes in GTF format |
|
| transcripts | Transcripts | Transcripts fasta file |
|
| proteins | Proteins | Proteins fasta file |
|
Version History
Version 1 (earliest) Created 23rd Nov 2020 at 16:22 by Bart Nijsse
Added/updated 1 files
Open
masterf8d3db7
Creators and SubmitterViews: 1051 Downloads: 33
Created: 23rd Nov 2020 at 16:22
Last used: 28th Nov 2022 at 08:16
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https://orcid.org/0000-0001-9524-5964
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