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

hapmers_blob_png (file)

Hap-mer blob plot

*.hapmers.blob.png
maintainers
Github user mahesh-panchal
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

merqury
PUBLIC DOMAIN

Evaluate genome assemblies with k-mers and more.

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