Description

k-mer based assembly evaluation.

Input

name:type
description
pattern

meta:map

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

meryl_db:file

Meryl read database

assembly:file

FASTA assembly file

Output

name:type
description
pattern

meta:map

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

versions:file

File containing software versions

versions.yml

assembly_only_kmers_bed:file

The positions of the k-mers found only in an assembly for further investigation in .bed

*_only.bed

assembly_only_kmers_wig:file

The positions of the k-mers found only in an assembly for further investigation in .wig

*_only.wig

stats:file

Assembly statistics file

*.completeness.stats

dist_hist:file

Histogram

*.dist_only.hist

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_cn_hist:file

Copy number spectra histogram

*.spectra-cn.hist

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_asm_hist:file

Assembly spectra histogram

*.spectra-asm.hist

assembly_qv:file

Assembly consensus quality estimation

*.qv

scaffold_qv:file

Scaffold consensus quality estimation

*.qv

read_ploidy:file

Ploidy estimate from read k-mer database

*.hist.ploidy

Tools

merqury
PUBLIC DOMAIN

Evaluate genome assemblies with k-mers and more.