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

]

`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

]

`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

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)

included in

maintainer

get in touch

Tools

merqury
PUBLIC DOMAIN

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)

included in

maintainer

get in touch

Tools

merqury PUBLIC DOMAIN

`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