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

]

reads (file)

Input file in FASTQ format.

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

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

assembly (file)

Assembled FASTA file

${prefix}_Assembly.fasta.gz

gfa (file)

Repeat graph

${prefix}_Assembly.gfa.gz

results (dir)

Resulting assembly directory

ShastaRun
maintainer
Github user fmalmeida
get in touch
Ask a question on Slack Open an issue on GitHub

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