Description

Evaluate a number of standard metrics for a genome assembly, including basic statistics, MerquryFK for completeness/QV scores, and BUSCO

Input

Name
Description
Pattern

ch_assemblies (file)

The input channel containing a list of assemblies for QC. The assemblies should be a list of haplotypes from the same genome.

Structure: [ val(meta), [path(asm1), path(asm2), ..., path(asm_n)] ]

*.{fa,fa.gz}

ch_fastk (file)

A channel containing FastK databases built from reads to compare the assemblies against in MerquryFK, and optionally with maternal and paternal FastK haptaps from MerquryFK's hapmaker tool.

Structure: [ val(meta), path(fastk_hist), path(fastk_ktabs), path(mat_ktabs), path(pat_ktabs) ]

*.{.hist,.ktab}

ch_busco_lineage (string)

The BUSCO lineage to use when assessing genome completeness with BUSCO. Either the name of a lineage (e.g. "lepidoptera_odb12") or one of "auto", "auto_euk", "auto_prok" to enable automatic lineage selection.

Structure: [ val(meta), string: busco_lineage ]

val_busco_lineage_directory (file)

A path to a local directory containing pre-downloaded BUSCO lineages.

Output

Name
Description
Pattern

asmstats (file)

Channel containing assembly statistics from asmstats. Structure: [ val(meta), path(stats) ]

*.stats

asmstats (file)

Channel containing assembly statistics from asmstats. Structure: [ val(meta), path(stats) ]

*.bam

busco_summary_txt (file)

BUSCO summary in txt format. Structure: [ val(meta), path(summary) ]

*.txt

busco_summary_json (file)

BUSCO summary in JSON format. Structure: [ val(meta), path(summary) ]

*.json

merqury_qv (file)

MerquryFK QV estimates for each assembly. Structure: [ val(meta), path(qv) ]

*.qv

merqury_completeness (file)

MerquryFK kmer completeness estimates for each assembly. Structure: [ val(meta), path(completeness) ]

*.completeness.stats

merqury_phased_stats (file)

MerquryFK kmer phasing estimates for each assembly. Structure: [ val(meta), path(phasing) ]

*.phased_block.stats

merqury_images (file)

MerquryFK plots - both CNI, ASM and phasing.

Structure: [ val(meta), path(image) ]

*.{png,pdf}

Components

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