Description

A tool to produce contig- and scaffold-level assembly statistics, including composition, length, N50 and L50 metrics.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

assembly (file)

Assembly fasta/gzipped fasta file

*.{fa,fa.gz}

Output

Name
Description
Pattern

stats

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.stats (file)

Plain text file containing assembly statistics

*.{stats}

versions_seqtk

${task.process} (string)

Name of the process

seqtk (string)

Name of the tool

seqtk |& sed "/Version/!d; s/.* //" (eval)

The expression to obtain the version of the tool

versions_asmstats

${task.process} (string)

Name of the process

asmstats (string)

Name of the tool

echo 1.0.0 (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

Name of the process

asmstats (string)

Name of the tool

echo 1.0.0 (eval)

The expression to obtain the version of the tool

${task.process} (string)

Name of the process

seqtk (string)

Name of the tool

seqtk |& sed "/Version/!d; s/.* //" (eval)

The expression to obtain the version of the tool

Tools

asmstats Documentation

A tool to produce contig- and scaffold-level assembly statistics, including composition, length, N50 and L50 metrics.

License: MIT
Pipelines with this module
genomeassembly
Authors