k-mer based assembly evaluation.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
meryl_db{:bash}
:file
Meryl read database
assembly{:bash}
FASTA assembly file
assembly_only_kmers_bed{:bash}
*_only.bed{:bash}
The positions of the k-mers found only in an assembly for further investigation in .bed
*_only.bed
assembly_only_kmers_wig{:bash}
*_only.wig{:bash}
The positions of the k-mers found only in an assembly for further investigation in .wig
*_only.wig
stats{:bash}
*.completeness.stats{:bash}
Assembly statistics file
*.completeness.stats
dist_hist{:bash}
*.dist_only.hist{:bash}
Histogram
*.dist_only.hist
spectra_cn_fl_png{:bash}
*.spectra-cn.fl.png{:bash}
Unstacked copy number spectra filled plot in PNG format
*.spectra-cn.fl.png
spectra_cn_hist{:bash}
*.spectra-cn.hist{:bash}
Copy number spectra histogram
*.spectra-cn.hist
spectra_cn_ln_png{:bash}
*.spectra-cn.ln.png{:bash}
Unstacked copy number spectra line plot in PNG format
*.spectra-cn.ln.png
spectra_cn_st_png{:bash}
*.spectra-cn.st.png{:bash}
Stacked copy number spectra line plot in PNG format
*.spectra-cn.st.png
spectra_asm_fl_png{:bash}
*.spectra-asm.fl.png{:bash}
Unstacked assembly spectra filled plot in PNG format
*.spectra-asm.fl.png
spectra_asm_hist{:bash}
*.spectra-asm.hist{:bash}
Assembly spectra histogram
*.spectra-asm.hist
spectra_asm_ln_png{:bash}
*.spectra-asm.ln.png{:bash}
Unstacked assembly spectra line plot in PNG format
*.spectra-asm.ln.png
spectra_asm_st_png{:bash}
*.spectra-asm.st.png{:bash}
Stacked assembly spectra line plot in PNG format
*.spectra-asm.st.png
assembly_qv{:bash}
${prefix}.qv{:bash}
Assembly consensus quality estimation
*.qv
scaffold_qv{:bash}
${prefix}.*.qv{:bash}
Scaffold consensus quality estimation
read_ploidy{:bash}
*.hist.ploidy{:bash}
Ploidy estimate from read k-mer database
*.hist.ploidy
hapmers_blob_png{:bash}
*.hapmers.blob.png{:bash}
Hap-mer blob plot
*.hapmers.blob.png
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Evaluate genome assemblies with k-mers and more.
