FastK based version of Merqury
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fastk_hist:file
A histogram files from the program FastK
*.hist
fastk_ktab:file
Histogram ktab files from the program FastK (option -t)
*.ktab*
assembly:file
Genome (primary) assembly files (fasta format)
.fasta
haplotigs:file
Assembly haplotigs (fasta format)
meta2:map
Groovy Map containing maternal sample information e.g. [ id:‘test’, single_end:false ]
mathaptab:file
trio maternal histogram ktab files from the program FastK (option -t)
meta3:map
Groovy Map containing paternal sample information e.g. [ id:‘test’, single_end:false ]
pathaptab:file
trio paternal histogram ktab files from the program FastK (option -t)
stats
${prefix}.completeness.stats:file
Assembly statistics file
*.completeness.stats
bed
${prefix}.*_only.bed:file
Assembly only kmer positions not supported by reads in bed format
*_only.bed
assembly_qv
${prefix}.*.qv:file
error and qv table for each scaffold of the assembly
*.qv
spectra_cn_fl
${prefix}.*.spectra-cn.fl.{png,pdf}:file
Unstacked copy number spectra filled plot in PNG or PDF format
*.spectra-cn.fl.{png,pdf}
spectra_cn_ln
${prefix}.*.spectra-cn.ln.{png,pdf}:file
Unstacked copy number spectra line plot in PNG or PDF format
*.spectra-cn.ln.{png,pdf}
spectra_cn_st
${prefix}.*.spectra-cn.st.{png,pdf}:file
Stacked copy number spectra line plot in PNG or PDF format
*.spectra-cn.st.{png,pdf}
qv
${prefix}.qv:file
error and qv of each assembly as a whole
spectra_asm_fl
${prefix}.spectra-asm.fl.{png,pdf}:file
Unstacked assembly spectra filled plot in PNG or PDF format
*.spectra-asm.fl.{png,pdf}
spectra_asm_ln
${prefix}.spectra-asm.ln.{png,pdf}:file
Unstacked assembly spectra line plot in PNG or PDF format
*.spectra-asm.ln.{png,pdf}
spectra_asm_st
${prefix}.spectra-asm.st.{png,pdf}:file
Stacked assembly spectra line plot in PNG or PDF format
*.spectra-asm.st.{png,pdf}
phased_block_bed
${prefix}.phased_block.bed:file
Assembly kmer positions separated by block in bed format
*.phased.block.bed
phased_block_stats
${prefix}.phased_block.stats:file
phased assembly statistics file
*.phased.block.stats
continuity_N
${prefix}.continuity.N.{pdf,png}:file
Stacked assembly N continuity plot in PNG or PDF format
*.continuity.N.{png,pdf}
block_N
${prefix}.block.N.{pdf,png}:file
Stacked assembly N continuity by block plot in PNG or PDF format
*.block.N.{png,pdf}
block_blob
${prefix}.block.blob.{pdf,png}:file
Stacked assembly block plot in PNG or PDF format
*.block.blob.{png,pdf}
hapmers_blob
${prefix}.hapmers.blob.{pdf,png}:file
Stacked assembly hapmers block plot in PNG or PDF format
*.hapmers.blob.{png,pdf}
versions
versions.yml:file
File containing software versions
versions.yml
