Description

SALSA, A tool to scaffold long read assemblies with HiC

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Fasta file of assembly. Headers must not contain ’:’

*.{fa, fasta}

index (file)

Fasta index file of assembly containing the length of contigs.

*.{fa.fai, fasta.fai}

bed (file)

BED file of alignments sorted by read names, e.g., from HiC-Pro

*.{bed}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Sequences for the scaffolds generated by the algorithm

*_scaffolds_FINAL.fasta

agp (file)

AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds

*_scaffolds_FINAL.agp

agp_original_coordinates (file)

Secondary output AGP file with names and coordinates matching the original input assembly (optional)

*scaffolds_FINAL.original-coordinates.agp

versions (file)

File containing software versions

versions.yml
maintainer
Github user scorreard
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

salsa2
MIT

Salsa is a tool to scaffold long read assemblies with Hi-C.

github.com/marbl/SALSA 10.1186/s12864-017-3879-z