CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities

• Published in: BMC bioinformatics Vol. 21; no. S12; pp. 303 - 7
• Main Authors: Kondratenko, Yulia, Korobeynikov, Anton, Lapidus, Alla
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 24.07.2020; BioMed Central; BMC
• Subjects: 16S metagenomics; Analysis; Annotations; Benchmarks; Clustering; Data analysis; Databases, Genetic; Datasets; Error correction & detection; High-Throughput Nucleotide Sequencing; Humans; Information management; Metagenomics; Microbiomes; Microbiota - genetics; Microorganisms; Molecular Sequence Annotation; Operational taxonomic units; Pipeline; Pipelines; Quality; Retrieval; RNA, Ribosomal, 16S - genetics; Software; Taxonomy; Utilities; Workflow; Workflow software; 16S metagenomics; Operational taxonomic units; Pipeline

Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis. In spite of development of several tools for merging of paired-end reads, poor quality at...