search

sanger-tol / genomenote

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
24 stars 6 forks source link

Base pair QV #11

Closed priyanka-surana closed 2 years ago

priyanka-surana commented 2 years ago

Description of feature

For Base QV, the information is under Base pair accuracy (QV) estimate. There are two methods: mapping based using longranger and kmer based using Merqury. As long as we have the meryl database, the kmer method is straight forward. There are also instructions to create meryl dbs: https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs

muffato commented 2 years ago

ToLA have settled on using FastK for the k-mer database, and a variant of Merqury that Yumi has pushed as a Docker image already: https://gitlab.internal.sanger.ac.uk/tol-it/software/docker-images/-/blob/main/fastk/Dockerfile#L32 Ksenia is often showing some QV stats from her work on the polishing pipeline. She can tell which software we should be using - for consistency.