Description

Whole-genome assembly using PacBio HiFi reads. This module is a modified version of the original nf-core version: https://github.com/nf-core/modules/blob/master/modules/nf-core/hifiasm/main.nf

Input

Name
Description
Pattern

meta (map)

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

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.

meta2 (map)

Groovy Map containing information about Hi-C reads

hic_cram (file)

Illumina short reads containing Hi-C data in unaligned CRAM format.

meta3 (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.

meta4 (map)

Groovy Map containing information about the input bin files

bin_files (file)

bin files produced during a previous Hifiasm run

meta5 (map)

Groovy Map containing information about the input bin files

previous_log (file)

log file to append to from a previous hifiasm run, e.g. if resuming from a bin files only run

Output

Name
Description
Pattern

bed

meta (map)

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

*.bed.gz (file)

BED files containing the co-ordinates of low-quality regions.

*.bed.gz

log

meta (map)

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

*.log (file)

Log file describing Hifiasm run.

*.log

bin_files

meta (map)

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

*.bin (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

read_overlaps

meta (map)

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

*.ovlp.paf.gz (file)

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

*.ovlp.paf.gz

assembly_fasta

meta (map)

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

*.fa (file)

Linearised assembly graphs in FASTA format

*.fa

assembly_graphs

meta (map)

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

*.gfa.gz (file)

Assembly graphs in GFA format

*.gfa.gz

corrected_reads

meta (map)

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

*.ec.fa.gz (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

versions_hifiasm

${task.process} (string)

Name of the process

hifiasm (string)

Name of the tool

hifiasm --version (eval)

The expression to obtain the version of the tool

versions_samtools

${task.process} (string)

Name of the process

samtools (string)

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

hifiasm (string)

The tool name

hifiasm --version (string)

The command used to generate the version of the tool

${task.process} (string)

Name of the process

samtools (string)

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //" (eval)

The expression to obtain the version of the tool

Tools

hifiasm Documentation

Haplotype-resolved assembler for accurate HiFi reads

doi: 10.1038/s41592-020-01056-5License: MIT
Pipelines with this module
genomeassembly
Authors