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Empirical studies

Per Unneberg

2023-12-21

Source: vignettes/empirical.Rmd
empirical.Rmd

Northern krill

genecovr was used to assess the quality metrics of the Northern krill genome.

To test genecovr with the 19 Gb Northern krill genome and gene data (16,509 transcripts of protein coding genes), access the collection in the SciLifeLab Data Repository named “Ecological genomics of the Northern krill” using the following permanent link:

< URL to be provided >

  1. Genome file

Access item: 1. Ecological genomics of the Northern krill: Genome assembly DNA sequences

Download: northern_krill.genome_assembly.tar.gz

Extract genome assembly for evaluation: 1.m_norvegica.main_w_mito.fasta

  1. Gene models

Access item: 3. Ecological genomics of the Northern krill: Genome assembly annotations (genes and repeats)

Download: trinity_transcript.16509_single_isoforms.cds.fasta.tar.gz

Extract and use transcripts for evaluation: trinity_transcript.16509_single_isoforms.cds.fasta

  1. gmap alignment

Map transcripts to assembly with gmap:

# Build index
gmap_build --genomedb mnorvegica 1.m_norvegica.main_w_mito.fasta
# Map with gmap; format=1 -> psl output
gmap -t 12 --dir . --db mnorvegica --format 1 trinity_transcript.16509_single_isoforms.cds.fasta > mnorvegica.psl
  1. genecovr input file

Generate a comma-separated file, assemblies.csv, with the following contents:

main,mnorvegica.psl,1.m_norvegica.main_w_mito.fasta,trinity_transcript.16509_single_isoforms.cds.fasta

and run

genecovr assemblies.csv

This will generate a number of summary data files along with png and pdf plots based on the summary data.