Description

Whole-genome assembly using PacBio HiFi reads

Input

name:type
description
pattern

meta{:bash}

:map

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

long_reads{:bash}

:file

Long reads PacBio HiFi reads or ONT reads (requires ext.arg ‘—ont’).

ul_reads{:bash}

:file

ONT long reads to use with —ul.

meta1{:bash}

:map

Groovy Map containing information about parental kmers.

paternal_kmer_dump{:bash}

:file

Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.

maternal_kmer_dump{:bash}

:file

Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.

meta2{:bash}

:map

Groovy Map containing information about Hi-C reads

hic_read1{:bash}

:file

Hi-C data Forward reads.

hic_read2{:bash}

:file

Hi-C data Reverse reads.

meta3{:bash}

:map

Groovy Map containing information about the input bin files

bin_files{:bash}

:file

bin files produced during a previous Hifiasm run

Output

name:type
description
pattern

raw_unitigs{:bash}

meta{:bash}

:map

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

*.r_utg.gfa{:bash}

:file

Raw unitigs

*.r_utg.gfa

bin_files{:bash}

meta{:bash}

:map

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

*.bin{:bash}

:file

Binary files containing processed data for hifiasm, including error-corrected reads, read overlaps, and Hi-C alignments. Can be re-used as an input for subsequent re-runs of hifiasm with new inputs or modified parameters in order to save recomputation of initial results, which are the most computationally-expensive steps.

*.bin

processed_unitigs{:bash}

meta{:bash}

:map

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

*.p_utg.gfa{:bash}

:file

Processed unitigs

*.p_utg.gfa

primary_contigs{:bash}

meta{:bash}

:map

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

${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa{:bash}

:file

Contigs representing the primary assembly

${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa

alternate_contigs{:bash}

meta{:bash}

:map

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

${prefix}.{a_ctg,hic.a_ctg}.gfa{:bash}

:file

Contigs representing the alternative assembly

${prefix}.{a_ctg,hic.a_ctg}.gfa

hap1_contigs{:bash}

meta{:bash}

:map

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

${prefix}.*.hap1.p_ctg.gfa{:bash}

:file

Contigs for the first haplotype. How the haplotypes are represented depends on the input mode; in standard HiFi-only mode, these are partially-phased parental contigs. In Hi-C mode, they are fully phased parental contigs, but the phasing is not maintained between contigs. In trio mode, they are fully phased paternal contigs all originating from a single parental haplotype.

${prefix}.*.hap1.p_ctg.gfa

hap2_contigs{:bash}

meta{:bash}

:map

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

${prefix}.*.hap2.p_ctg.gfa{:bash}

:file

Contigs for the second haplotype. How the haplotypes are represented depends on the input mode; in standard HiFi-only mode, these are partially-phased parental contigs. In Hi-C mode, they are fully phased parental contigs, but the phasing is not maintained between contigs. In trio mode, they are fully phased paternal contigs all originating from a single parental haplotype.

${prefix}.*.hap2.p_ctg.gfa

corrected_reads{:bash}

meta{:bash}

:map

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

*.ec.fa.gz{:bash}

:file

If option —write-ec specified, a gzipped fasta file containing the error corrected reads produced by the hifiasm error correction module

*.ec.fa.gz

read_overlaps{:bash}

meta{:bash}

:map

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

*.ovlp.paf.gz{:bash}

:file

If option —write-paf specified, a gzipped paf file describing the overlaps among all error-corrected reads

*.ovlp.paf.gz

log{:bash}

meta{:bash}

:map

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

${prefix}.stderr.log{:bash}

:file

Stderr log

*.stderr.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

hifiasm
MIT

Haplotype-resolved assembler for accurate HiFi reads

github.com/chhylp123/hifiasm 10.1038/s41592-020-01056-5
included in
genomeassembler
maintainers
Github user sidorov-si
Github user scorreard
get in touch
Ask a question on Slack Open an issue on GitHub