Description

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296.

Input

name:type
description
pattern

meta

:map

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

reads

:file

Input file in FASTQ format.

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

model

:string

Shasta assembly configuration model name (e.g. ‘Nanopore-Oct2021’, ‘Nanopore-Dec2019’)

Output

name:type
description
pattern

assembly

meta

:map

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

*_Assembly.fasta.gz

:file

Assembled FASTA file

${prefix}_Assembly.fasta.gz

gfa

meta

:map

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

*_Assembly.gfa.gz

:file

Repeat graph

${prefix}_Assembly.gfa.gz

results

meta

:map

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

ShastaRun/

:directory

Resulting assembly directory

ShastaRun

versions_shasta

${task.process}

:string

The name of the process

shasta

:string

The name of the tool

shasta --version | sed -n '1s/.* //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

shasta

:string

The name of the tool

shasta --version | sed -n '1s/.* //p'

:eval

The expression to obtain the version of the tool

Tools

shasta
MIT

Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

chanzuckerberg.github.io/shasta https://github.com/chanzuckerberg/shasta 10.1038/s41587-020-0503-6
maintainer
Github user fmalmeida
get in touch
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