Analysis of Metabarcoding experiments using Lotus 1.64 - quadram-institute-bioscience/gmh-sops GitHub Wiki

Methods

Preprocessing of reads

The quality profiles of the sequencing output has been assessed with Fastp 0.20.0 [1], oer and the presence of the expected sequencing primers with SeqFu 0.96 [3].

Analysis of 16S and ITS sequencing

References

1. 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;
2. Martin M. Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads. DOI: 10.14806/ej.17.1.200
3. 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; PMCID: PMC8148589.
4. Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J. LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome. 2014 Sep;2(1):30. DOI: 10.1186/2049-2618-2-30. PMID: 27367037