Description

FastK based version of Merqury

Input

name:type
description
pattern

meta:map

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

]

fastk_hist:file

A histogram files from the program FastK

*.hist

fastk_ktab:file

Histogram ktab files from the program FastK (option -t)

*.ktab*

assembly:file

Genome (primary) assembly files (fasta format)

.fasta

haplotigs:file

Assembly haplotigs (fasta format)

.fasta

matktab:file

trio maternal histogram ktab files from the program FastK (option -t)

*.ktab*

patktab:file

trio paternal histogram ktab files from the program FastK (option -t)

*.ktab*

Output

name:type
description
pattern

stats

meta:map

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

]

${prefix}.completeness.stats:file

Assembly statistics file

*.completeness.stats

bed

meta:map

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

]

${prefix}.*_only.bed:file

Assembly only kmer positions not supported by reads in bed format

*_only.bed

assembly_qv

meta:map

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

]

${prefix}.*.qv:file

error and qv table for each scaffold of the assembly

*.qv

spectra_cn_fl

meta:map

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

]

${prefix}.*.spectra-cn.fl.{png,pdf}:file

Unstacked copy number spectra filled plot in PNG or PDF format

*.spectra-cn.fl.{png,pdf}

spectra_cn_ln

meta:map

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

]

${prefix}.*.spectra-cn.ln.{png,pdf}:file

Unstacked copy number spectra line plot in PNG or PDF format

*.spectra-cn.ln.{png,pdf}

spectra_cn_st

meta:map

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

]

${prefix}.*.spectra-cn.st.{png,pdf}:file

Stacked copy number spectra line plot in PNG or PDF format

*.spectra-cn.st.{png,pdf}

qv

meta:map

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

]

${prefix}.qv:file

error and qv of each assembly as a whole

*.qv

spectra_asm_fl

meta:map

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

]

${prefix}.spectra-asm.fl.{png,pdf}:file

Unstacked assembly spectra filled plot in PNG or PDF format

*.spectra-asm.fl.{png,pdf}

spectra_asm_ln

meta:map

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

]

${prefix}.spectra-asm.ln.{png,pdf}:file

Unstacked assembly spectra line plot in PNG or PDF format

*.spectra-asm.ln.{png,pdf}

spectra_asm_st

meta:map

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

]

${prefix}.spectra-asm.st.{png,pdf}:file

Stacked assembly spectra line plot in PNG or PDF format

*.spectra-asm.st.{png,pdf}

phased_block_bed

meta:map

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

]

${prefix}.phased_block.bed:file

Assembly kmer positions seperated by block in bed format

*.phased.block.bed

phased_block_stats

meta:map

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

]

${prefix}.phased_block.stats:file

phased assembly statistics file

*.phased.block.stats

continuity_N

meta:map

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

]

${prefix}.continuity.N.{pdf,png}:file

Stacked assembly N continuity plot in PNG or PDF format

*.continuity.N.{png,pdf}

block_N

meta:map

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

]

${prefix}.block.N.{pdf,png}:file

Stacked assembly N continuity by block plot in PNG or PDF format

*.block.N.{png,pdf}

block_blob

meta:map

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

]

${prefix}.block.blob.{pdf,png}:file

Stacked assembly block plot in PNG or PDF format

*.block.blob.{png,pdf}

hapmers_blob

meta:map

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

]

${prefix}.hapmers.blob.{pdf,png}:file

Stacked assembly hapmers block plot in PNG or PDF format

*.hapmers.blob.{png,pdf}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

merquryfk
https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE

FastK based version of Merqury