Description

Map short-reads to an indexed reference genome

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory)

*.{bam,cram,fastq,fastq.gz,fq,fq.gz}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘test’, single_end:false ]

index{:bash}

:file

mapAD genome index files (mandatory)

*.{tbw,tle,toc,tos,tpi,trt,tsa}

mismatch_parameter{:bash}

:float

Minimum probability of the number of mismatches under -D base error rate

double_stranded_library{:bash}

:boolean

Library preparation method - specify if double stranded else it’s assumed single stranded

five_prime_overhang{:bash}

:float

5’-overhang length parameter

three_prime_overhang{:bash}

:float

3’-overhang length parameter

deam_rate_double_stranded{:bash}

:float

Deamination rate in double-stranded stem of a read

deam_rate_single_stranded{:bash}

:float

Deamination rate in single-stranded ends of a read

indel_rate{:bash}

:float

Expected rate of indels between reads and reference

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

Output BAM/SAM file containing read alignments

*.bam

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

mapad
MIT

An aDNA aware short-read mapper

github.com/mpieva/mapAD
maintainer
Github user jch-13
get in touch
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