nQuire is a software program (Weiß et al. 2018) that estimates sample ploidy levels from next-generation sequencing (NGS; e.g. Illumina) reads for one or multiple samples, starting from BAM file(s) (extension '.bam'; Li et al. 2009) for the sample(s). It is assumed that the .bam input file(s) were output by an aligner such as bwa (Li and Durbin 2009) and contain information on reads mapped to an appropriate reference (draft reference genome, pseudo-reference genome assembly, etc.). Find the nQuire paper here or using the reference below.
nQuire is available through a GitHub repository, and installation instructions are given in the main README for the repo. I have had success installing nQuire, following the given instructions, on both macOS High Sierra v10.13+ and CentOS 6/7 Linux OS's.
git clone --recursive https://github.com/clwgg/nQuire
cd nQuire/
make submodules
make
I have written a wrapper script, nQuireRunner, that I am testing for PIrANHA, and that I will soon be adding as a function in the next PIrANHA release. This script automates running nQuire on one or multiple BAM files in the current working directory.
- Li, H., Durbin, R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.
- Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 1000 Genome Project Data Processing Subgroup 2009. The sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079.
- Weiß, C.L., Pais, M., Cano, L.M., Kamoun, S. Burbano, H.A. 2018. nQuire: a statistical framework for ploidy estimation using next generation sequencing. BMC bioinformatics, 19(1), 122.