Description

TransDecoder identifies 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

pep

meta:map

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

]

${output_dir_name}/*.pep:file

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

*.{pep}

gff3

meta:map

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

]

${output_dir_name}/*.gff3:file

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

*.{gff3}

cds

meta:map

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

]

${output_dir_name}/*.cds:file

the nucleotide coding sequence for all detected ORFs. file

*{cds}

dat

meta:map

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

]

${output_dir_name}/*.dat:file

nucleotide frequencies

*{dat}

folder

${output_dir_name}:directory

contains all the files from the run

versions

versions.yml:file

File containing software versions

versions.yml

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
included in
metatdenovo
maintainer
Github user Danilo2771
get in touch
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