modules/merqury

k-mer based assembly evaluation.

k-merassemblyevaluation

https://github.com/nf-core/modules/[...]/modules/nf-core/merqury

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.

https://github.com/marbl/merqury 10.1186/s13059-020-02134-9

included in

maintainer

get in touch

Ask a question on Slack Open an issue on GitHub

modules/merqury

Description

Input

meta:map

meryl_db:file

assembly:file

Output

meta:map

versions:file

assembly_only_kmers_bed:file

assembly_only_kmers_wig:file

stats:file

dist_hist:file

spectra_cn_fl_png:file

spectra_cn_ln_png:file

spectra_cn_st_png:file

spectra_cn_hist:file

spectra_asm_fl_png:file

spectra_asm_ln_png:file

spectra_asm_st_png:file

spectra_asm_hist:file

assembly_qv:file

scaffold_qv:file

read_ploidy:file

Tools

merqury PUBLIC DOMAIN

included in

maintainer

get in touch

`meta:map`

`meryl_db:file`

`assembly:file`

`meta:map`

`versions:file`

`assembly_only_kmers_bed:file`

`assembly_only_kmers_wig:file`

`stats:file`

`dist_hist:file`

`spectra_cn_fl_png:file`

`spectra_cn_ln_png:file`

`spectra_cn_st_png:file`

`spectra_cn_hist:file`

`spectra_asm_fl_png:file`

`spectra_asm_ln_png:file`

`spectra_asm_st_png:file`

`spectra_asm_hist:file`

`assembly_qv:file`

`scaffold_qv:file`

`read_ploidy:file`

merqury
PUBLIC DOMAIN