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: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}
gfa:file
GFA file of the assembly graph
dup:file
File containing the duplicated contigs
filter_bed:file
BED file of the filtered alignments
fasta
*_scaffolds_FINAL.fasta:file
Sequences for the scaffolds generated by the algorithm
*_scaffolds_FINAL.fasta
agp
*_scaffolds_FINAL.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
*/*scaffolds_FINAL.original-coordinates.agp:file
Secondary output AGP file with names and coordinates matching the original input assembly (optional)
*scaffolds_FINAL.original-coordinates.agp
versions
versions.yml:file
File containing software versions
versions.yml
Salsa is a tool to scaffold long read assemblies with Hi-C.
