wms 2020 - quadram-institute-bioscience/gmh-sops GitHub Wiki

Methods

Raw sequences have been quality checked with SeqFu 1.8.5 (Telatin 2021) and filtered using Fastp (Chen 2018) to remove sequences with any bases below Phred 15. Human reads have been filtered using Kraken 2 (Wood 2019) against the Human genome (release hg19).

Taxonomic profiling of the filtered reads has been performed using Kraken2 and Bracken (Lu 2016) against the a database containing archaea, bacteria, viral, plasmid, human1, UniVec_Core, Protozoa and Fungi ("PlusPF" from https://benlangmead.github.io/aws-indexes/k2).

Reports of the results has been generated using MultiQC (Ewels 2016). All the tools have been retrieved from the BioConda (Grüning 2018) repository.

References

  • Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering (Basel, Switzerland). 2021 May;8(5). DOI: 10.3390/bioengineering8050059. PMID: 34066939
  • Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England). 2018 Sep;34(17):i884-i890. DOI: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281.
  • Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biology. 2019 Nov;20(1):257. DOI: 10.1186/s13059-019-1891-0. PMID: 31779668; PMCID: PMC6883579.
  • Lu J, Breitwieser FP, Thielen P, Salzberg SL. Bracken: Estimating species abundance in metagenomics data. bioRxiv; 2016. DOI: 10.1101/051813.
  • Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics (Oxford, England). 2016 Oct;32(19):3047-3048. DOI: 10.1093/bioinformatics/btw354. PMID: 27312411; PMCID: PMC5039924.
  • Grüning B, Dale R, Sjödin A, et al. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods. 2018 Jul;15(7):475-476. DOI: 10.1038/s41592-018-0046-7. PMID: 29967506.
  • Kraken2 databases, https://benlangmead.github.io/aws-indexes/k2