Description

Assembles a small genome (bacterial, fungal, viral)

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

3 ()

yml (file)

Path to yml file containing read information. The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) in addition to this YML. File entries in this yml must contain only the file name and no paths.

*.{yml,yaml}

hmm (file)

File or directory with amino acid HMMs for Spades HMM-guided mode.

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

spades Documentation

SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

https://github.com/ablab/spadesdoi: 10.1089/cmb.2012.0021License: GPL v2
Authors