Performs assembly scaffolding using YaHS
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
fasta{:bash}
:file
FASTA reference file
*.{fasta,fa}
fai{:bash}
index of the reference file
*.{fai}
hic_map{:bash}
BED file containing coordinates of read alignments
*.{bed,bam,bin}
agp{:bash}
Optional AGP file describing a set of scaffolds from the input contigs to use as a start point
*.agp
scaffolds_fasta{:bash}
${prefix}_scaffolds_final.fa{:bash}
FASTA file with resulting contigs
${prefix}_scaffolds_final.fa
scaffolds_agp{:bash}
${prefix}_scaffolds_final.agp{:bash}
AGP file containing contigs placing coordinates
${prefix}_scaffolds_final.agp
initial_break_agp{:bash}
${prefix}_{inital,no}_break*.agp{:bash}
AGP file describing initial contig breaks
${prefix}_{inital,no}_break*.agp
round_agp{:bash}
${prefix}_r*_*.agp{:bash}
AGP file describing intermediate rounds of scaffolding
${prefix}_{initial,no}_break*.agp
binary{:bash}
${prefix}.bin{:bash}
Binary data file with alignment results of Hi-C reads to the contigs in internal YaHS binary format
${prefix}.bin
log{:bash}
${prefix}.log{:bash}
Log file describing YaHS run
${prefix}.log
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
YaHS, yet another Hi-C scaffolding tool.
