Merqury - Evaluate genome assemblies with k-mers and more
Often, genome assembly projects have illumina whole genome sequencing reads
available for the assembled individual. The k-mer spectrum of this read set can
be used for independently evaluating assembly quality without the need of a high
quality reference. Merqury provides a set of tools for this purpose.
Location and version:
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$ which merqury.sh
/local/cluster/bin/merqury.sh
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help message:
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$ merqury.sh
Usage: merqury.sh <read-db.meryl> [<mat.meryl> <pat.meryl>] <asm1.fasta> [asm2.fasta] <out>
<read-db.meryl> : k-mer counts of the read set
<mat.meryl> : k-mer counts of the maternal haplotype (ex. mat.hapmer.meryl)
<pat.meryl> : k-mer counts of the paternal haplotype (ex. pat.hapmer.meryl)
<asm1.fasta> : Assembly fasta file (ex. pri.fasta, hap1.fasta or maternal.fasta)
[asm2.fasta] : Additional fasta file (ex. alt.fasta, hap2.fasta or paternal.fasta)
*asm1.meryl and asm2.meryl will be generated. Avoid using the same names as the hap-mer dbs
<out> : Output prefix
Arang Rhie, 2020-01-29. arrhie@gmail.com
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software ref: https://github.com/marbl/merqury
research ref: https://doi.org/10.1186/s13059-020-02134-9