Whole-genome assembly using PacBio HiFi reads
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
long_reads:file
Long reads PacBio HiFi reads or ONT reads (requires ext.arg ‘—ont’).
ul_reads:file
ONT long reads to use with —ul.
meta1:map
Groovy Map containing information about parental kmers.
paternal_kmer_dump:file
Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
maternal_kmer_dump:file
Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
meta2:map
Groovy Map containing information about Hi-C reads
hic_read1:file
Hi-C data Forward reads.
hic_read2:file
Hi-C data Reverse reads.
raw_unitigs
*.r_utg.gfa:file
Raw unitigs
*.r_utg.gfa
corrected_reads
*.ec.bin:file
Corrected reads
*.ec.bin
source_overlaps
*.ovlp.source.bin:file
Source overlaps
*.ovlp.source.bin
reverse_overlaps
*.ovlp.reverse.bin:file
Reverse overlaps
*.ovlp.reverse.bin
processed_contigs
*.bp.p_ctg.gfa:file
Processed contigs
*.bp.p_ctg.gfa
processed_unitigs
*.p_utg.gfa:file
Processed unitigs
*.p_utg.gfa
primary_contigs
*.asm.p_ctg.gfa:file
Primary contigs
*.asm.p_ctg.gfa
alternate_contigs
*.asm.a_ctg.gfa:file
Alternative contigs
*.asm.a_ctg.gfa
paternal_contigs
*.hap1.p_ctg.gfa:file
Paternal contigs
*.hap1.p_ctg.gfa
maternal_contigs
*.hap2.p_ctg.gfa:file
Maternal contigs
*.hap2.p_ctg.gfa
log
*.log:file
Stderr log
*.log
versions
versions.yml:file
File containing software versions
versions.yml
Haplotype-resolved assembler for accurate HiFi reads
