Description

NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

:file

fastq.gz files

*.fastq.gz

meta2{:bash}

:map

Groovy Map containing fasta information

fasta{:bash}

:file

reference fasta file - must be unzipped

*.fasta

meta3{:bash}

:map

Groovy Map containing index information

index{:bash}

:file

reference BWA index

*.{amb,ann,bwt,pac,sa}

known_sites{:bash}

:file

(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.

*.vcf.gz

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

Sorted BAM file

*.bam

bai{:bash}

meta{:bash}

:map

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

*.bai{:bash}

:file

index corresponding to sorted BAM file

*.bai

qc_metrics{:bash}

qc_metrics{:bash}

:directory

(optional) optional directory of qc metrics

qc_metrics

bqsr_table{:bash}

*.table{:bash}

:file

(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr

*.table

duplicate_metrics{:bash}

duplicate-metrics.txt{:bash}

:file

(optional) metrics calculated from marking duplicates in the bam file

*-duplicate-metrics.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/latest
included in
methylseq
maintainers
Github user sateeshperi
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub