modules/hifiasm

Whole-genome assembly using PacBio HiFi reads

genome assemblyhaplotype resolutionphasingPacBioHiFilong reads

https://github.com/nf-core/modules/[...]/modules/nf-core/hifiasm

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: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.

`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.

`meta3:map`

Groovy Map containing information about the input bin files

`bin_files:file`

bin files produced during a previous Hifiasm run

Output

name:type

description

pattern

`raw_unitigs`

`meta:map`

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

`*.r_utg.gfa:file`

Raw unitigs

*.r_utg.gfa

`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

`processed_unitigs`

`meta:map`

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

`*.p_utg.gfa:file`

Processed unitigs

*.p_utg.gfa

`primary_contigs`

`meta:map`

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

`${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa:file`

Contigs representing the primary assembly

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

`alternate_contigs`

`meta:map`

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

`${prefix}.{a_ctg,hic.a_ctg}.gfa:file`

Contigs representing the alternative assembly

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

`hap1_contigs`

`meta:map`

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

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

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

`meta:map`

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

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

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

`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

`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

`log`

`meta:map`

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

*.stderr.log

`${prefix}.stderr.log:file`

Stderr log

*.stderr.log

`versions`

`versions.yml: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

modules/hifiasm

Description

Input

meta:map

long_reads:file

ul_reads:file

meta1:map

paternal_kmer_dump:file

maternal_kmer_dump:file

meta2:map

hic_read1:file

hic_read2:file

meta3:map

bin_files:file

Output

raw_unitigs

meta:map

*.r_utg.gfa:file

bin_files

meta:map

*.bin:file

processed_unitigs

meta:map

*.p_utg.gfa:file

primary_contigs

meta:map

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

alternate_contigs

meta:map

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

hap1_contigs

meta:map

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

hap2_contigs

meta:map

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

corrected_reads

meta:map

*.ec.fa.gz:file

read_overlaps

meta:map

*.ovlp.paf.gz:file

log

meta:map

${prefix}.stderr.log:file

versions

versions.yml:file

Tools

hifiasm MIT

`meta:map`

`long_reads:file`

`ul_reads:file`

`meta1:map`

`paternal_kmer_dump:file`

`maternal_kmer_dump:file`

`meta2:map`

`hic_read1:file`

`hic_read2:file`

`meta3:map`

`bin_files:file`

`raw_unitigs`

`meta:map`

`*.r_utg.gfa:file`

`bin_files`

`meta:map`

`*.bin:file`

`processed_unitigs`

`meta:map`

`*.p_utg.gfa:file`

`primary_contigs`

`meta:map`

`${prefix}.{p_ctg,bp.p_ctg,hic.p_ctg}.gfa:file`

`alternate_contigs`

`meta:map`

`${prefix}.{a_ctg,hic.a_ctg}.gfa:file`

`hap1_contigs`

`meta:map`

`${prefix}.*.hap1.p_ctg.gfa:file`

`hap2_contigs`

`meta:map`

`${prefix}.*.hap2.p_ctg.gfa:file`

`corrected_reads`

`meta:map`

`*.ec.fa.gz:file`

`read_overlaps`

`meta:map`

`*.ovlp.paf.gz:file`

`log`

`meta:map`

`${prefix}.stderr.log:file`

`versions`

`versions.yml:file`

hifiasm
MIT