0. Software and data

BioLinux

For the course we will use a modified version of BioLinux where all tools and data for the course are already installed. The user details for the BioLinux image are:

user: manager
pass: manager

Tools

For the course we are going to use the following tools:

Quality control

FastQC

BBtools

Read merging

PEAR

BBtools

Gene prediction

FragGeneScan

Prodigal

rRNA identification

SortMeRNA

SILVAngs

Online metagenomic resources

MG-RAST

EBI Metagenomics Portal

Fast similarity search

Diamond

Metagenomic assembly

Megahit

IDBA_UD

(Meta)genomic annotation

PROKKA

Short-read mapping

BWA

Tools for high-throughput sequencing data

A fork from Samtools

Picard

Bedops

Bedtools

Data

Details for the OSD102 site metagenome can be found here