SALSA, A tool to scaffold long read assemblies with HiC
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta
:file
Fasta file of assembly. Headers must not contain ’:’
*.{fa, fasta}
index
Fasta index file of assembly containing the length of contigs.
*.{fa.fai, fasta.fai}
bed
BED file of alignments sorted by read names, e.g., from HiC-Pro
*.{bed}
gfa
GFA file of the assembly graph
dup
File containing the duplicated contigs
filter_bed
BED file of the filtered alignments
*_scaffolds_FINAL.fasta
Sequences for the scaffolds generated by the algorithm
agp
*_scaffolds_FINAL.agp
AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds
agp_original_coordinates
*/*scaffolds_FINAL.original-coordinates.agp
Secondary output AGP file with names and coordinates matching the original input assembly (optional)
*scaffolds_FINAL.original-coordinates.agp
versions
versions.yml
File containing software versions
Salsa is a tool to scaffold long read assemblies with Hi-C.
