Description

TransDecoder itentifies candidate coding regions within transcript sequences. it is used to build gff file.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

fasta file

*.{fasta}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

pep (Amino acids fasta file)

all ORFs meeting the minimum length criteria, regardless of coding potential. file

*.{pep}

gff3 (gff file)

positions of all ORFs as found in the target transcripts. file

*.{gff3}

cds (fasta file)

the nucleotide coding sequence for all detected ORFs. file

*{cds}

dat (tsv file)

nucleotide frequencies

*{dat}

folder (directory)

contains all the files from the run

included in
metatdenovo
author
Github user Danilo2771
get in touch
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Tools

transdecoder
Broad Institute

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

github.com/TransDecoder github.com/TransDecoder/TransDecoder/wiki https://github.com/TransDecoder/TransDecoder