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 >
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
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
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
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.
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