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