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

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

stats (file)

Assembly statistics file

*.completeness.stats

bed (file)

Assembly only kmer positions not supported by reads in bed format

*_only.bed

spectra_cn_fl_png (file)

Unstacked copy number spectra filled plot in PNG format

*.spectra-cn.fl.png

spectra_cn_ln_png (file)

Unstacked copy number spectra line plot in PNG format

*.spectra-cn.ln.png

spectra_cn_st_png (file)

Stacked copy number spectra line plot in PNG format

*.spectra-cn.st.png

spectra_asm_fl_png (file)

Unstacked assembly spectra filled plot in PNG format

*.spectra-asm.fl.png

spectra_asm_ln_png (file)

Unstacked assembly spectra line plot in PNG format

*.spectra-asm.ln.png

spectra_asm_st_png (file)

Stacked assembly spectra line plot in PNG format

*.spectra-asm.st.png

spectra_cn_fl_pdf (file)

Unstacked copy number spectra filled plot in PDF format

*.spectra-cn.fl.pdf

spectra_cn_ln_pdf (file)

Unstacked copy number spectra line plot in PDF format

*.spectra-cn.ln.pdf

spectra_cn_st_pdf (file)

Stacked copy number spectra line plot in PDF format

*.spectra-cn.st.pdf

spectra_asm_fl_pdf (file)

Unstacked assembly spectra filled plot in PDF format

*.spectra-asm.fl.pdf

spectra_asm_ln_pdf (file)

Unstacked assembly spectra line plot in PDF format

*.spectra-asm.ln.pdf

spectra_asm_st_pdf (file)

Stacked assembly spectra line plot in PDF format

*.spectra-asm.st.pdf

assembly_qv (file)

error and qv table for each scaffold of the assembly

*.qv

qv (file)

error and qv of each assembly as a whole

*.qv

Tools

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

FastK based version of Merqury