Description

Compare k-mer frequency in reads and assembly to devise the metrics K and QV

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

1 ()

lookup_table (file)

Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL]

lookup_table.txt

seqmers (file)

Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL]

*.{meryl_db}

peak (float)

Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED]

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

merfin Documentation

Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of Merqury) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads.

doi: 10.1038/s41592-022-01445-yLicense: Apache-2.0
Authors