Workflow: Find reads with predicted coding sequences above 60 AA in length

Fetched 2021-01-17 21:00:32 GMT
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Inputs

ID Type Title Doc
sequence File [FASTA]
model https://w3id.org/cwl/view/git/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/tools/FragGeneScan-model.yaml#model
completeSeq Boolean

Steps

ID Runs Label Doc
combine_predicted_CDS_aa
../tools/concatenate.cwl (CommandLineTool)
split_seqs
../tools/fasta_chunker.cwl (CommandLineTool)
split FASTA by number of records

based upon code by Maxim Scheremetjew, EMBL-EBI

ORF_prediction
../tools/FragGeneScan1_20.cwl (CommandLineTool)
FragGeneScan: find (fragmented) genes in short reads

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013 (https://sourceforge.net/projects/fraggenescan/).

Version 1.20 can be downloaded here: https://sourceforge.net/projects/fraggenescan/files/

combine_predicted_CDS_nuc
../tools/concatenate.cwl (CommandLineTool)

Outputs

ID Type Label Doc
predicted_CDS_nuc File [FASTA]
predicted_CDS_aa File [FASTA]
Permalink: https://w3id.org/cwl/view/git/6430df56f7345f837d3f9c3f7fb5af5aa9dadc90/workflows/orf_prediction.cwl