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

Fetched 2020-07-14 13:50:33 GMT
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Inputs

ID Type Title Doc
sequence File [FASTA]
completeSeq Boolean
model https://w3id.org/cwl/view/git/5dc7c5ca618a248a99bd4bf5f3042cdb21947193/tools/FragGeneScan-model.yaml#model

Steps

ID Runs Label Doc
remove_short_pCDS
../tools/discard_short_seqs.cwl (CommandLineTool)
drop short seqs
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/

Outputs

ID Type Label Doc
predictedCDS File [FASTA]
Permalink: https://w3id.org/cwl/view/git/5dc7c5ca618a248a99bd4bf5f3042cdb21947193/workflows/orf_prediction.cwl