Description

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

FASTA or FASTQ files

*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}

fasta (file)

Reference genome FASTA file used to construct Segemehl

*.{fa,fasta}

index (file)

Segemehl Index file from SEGEMEHL_INDEX

*.idx

Output

Name (Type)
Description
Pattern

meta (map)

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

]

results (directory)

Directory containing genomic alignments in SAM format
(please add “-b” flag to task.ext.args for BAM)
In addition to split-read alignments files when -S parameter used.
[ *.{sam,bam}, *.trns.txt, *.mult.bed, *.sngl.bed ]

${meta.id}*

versions (file)

File containing software versions

versions.yml
included in
circrna
mantainer
Github user BarryDigby
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Tools

segemehl
GPL v3

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

bioinf.uni-leipzig.de/Software/segemehl10.1186/gb-2014-15-2-r34