Description

Scaffold an assembly FASTA file using Hi-C contacts with YaHS.

Input

Name
Description
Pattern

ch_fasta (file)

Channel containing assemblies for scaffolding. Structure: [ val(meta), path(fasta) ]

*.{bam/cram/sam}

ch_hic_bam (file)

Channel containing BAM files of Hi-C reads mapped to each assembly. Structure: [ val(meta), path(bam) ]

*.{bam/cram/sam}

Output

Name
Description
Pattern

scaffolds_fasta (file)

Final scaffolds from YaHS in FASTA format Structure: [ val(meta), path(fasta) ]

*.fasta

scaffolds_agp (file)

AGP describing how contigs are transformed into final scaffolds Structure: [ val(meta), path(agp) ]

*.agp

scaffolds_pairs (file)

Pairs file describing Hi-C contacts between scaffolds, translated from the contigs pairs file Structure: [ val(meta), path(pairs) ]

*.pairs.gz

scaffolds_chromsizes (file)

Chromsizes file for the scaffolds. A headerless TSV of format <contigname>\t<size> Structure: [ val(meta), path(chromsizes) ]

*.sizes

yahs_bin (file)

YaHS binary file describing Hi-C contacts Structure: [ val(meta), path(bin) ]

*.bin

yahs_initial (file)

AGP files describing inital breaks by YaHS Structure: [ val(meta), path(agp) ]

*.agp

yahs_intermediate (file)

AGP files describing each scaffolding round by YaHS Structure: [ val(meta), path(agp) ]

*.agp

yahs_log (file)

YaHS log file Structure: [ val(meta), path(log) ]

*.log

Components

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