Description

Whole-genome assembly using PacBio HiFi reads

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

FASTQ file with PacBio HiFi reads

*.{fastq}

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.

use_parental_kmers (boolean)

A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps.

hic_read1 (file)

Hi-C data Forward reads.

hic_read2 (file)

Hi-C data Reverse reads.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

raw_unitigs (file)

Raw unitigs

*.r_utg.gfa

processed_unitigs (file)

Processed unitigs

*.p_utg.gfa

primary_contigs (file)

Primary contigs

*.asm.p_ctg.gfa

alternate_contigs (file)

Alternative contigs

*.asm.a_ctg.gfa

paternal_contigs (file)

Paternal contigs

*.hap1.p_ctg.gfa

maternal_contigs (file)

Maternal contigs

*.hap2.p_ctg.gfa

corrected_reads (file)

Corrected reads

*.ec.bin

source_overlaps (file)

Source overlaps

*.ovlp.source.bin

reverse_overlaps (file)

Reverse overlaps

*.ovlp.reverse.bin

log (file)

Stderr log

*.log
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Tools

hifiasm
MIT

Haplotype-resolved assembler for accurate HiFi reads

github.com/chhylp123/hifiasm 10.1038/s41592-020-01056-5