Description

Map short-reads to an indexed reference genome

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (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 (map)

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

]

index (file)

mapAD genome index files (mandatory)

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

mismatch_parameter (float)

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

double_stranded_library (boolean)

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

five_prime_overhang (float)

5’-overhang length parameter

three_prime_overhang (float)

3’-overhang length parameter

deam_rate_double_stranded (float)

Deamination rate in double-stranded stem of a read

deam_rate_single_stranded (float)

Deamination rate in single-stranded ends of a read

indel_rate (float)

Expected rate of indels between reads and reference

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

bam (file)

Output BAM/SAM file containing read alignments

*.bam
maintainer
Github user jch-13
get in touch
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Tools

mapad
MIT

An aDNA aware short-read mapper

github.com/mpieva/mapAD