Computational protocol: A catalogue of 136 microbial draft genomes from Red Sea metagenomes

Similar protocols

Protocol publication

[…] Seawater samples were collected from eight stations and from different depths (10, 25, 50, 100, 200, and 500 m; locations are shown in ) during summer as part of KRSE2011 (ref. ). Genomic DNA was extracted from the 0.1–1.2 μm size fraction using an established phenol-chloroform extraction protocol,. Paired-end libraries (2×100 bp) were prepared using Nextera DNA Library Prep Kit (Illumina) and sequenced on a HiSeq 2000 (Illumina). Reads were quality checked and trimmed using PRINSEQ v0.20.4 (ref. ) generating read lengths of ~93 bp and a total of ~10 million reads per sample with median insert sizes ranging from 183–366 bp (Data Citation 1). Trimmed metagenome reads were individually assembled ( (available online only)) using IDBA-UD v1.1.1 (ref. ) using the ‘--pre-correction’ option. To obtain coverage profile of contigs from each metagenomic assembly, the trimmed reads were mapped back to contigs using BWA v0.7.12 (ref. ) with the bwa-mem algorithm. […]

Pipeline specifications

Software tools PRINSEQ, IDBA-UD, BWA
Application Metagenomic sequencing analysis