0. Software and data

Tools

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

Quality control

FastQC
BBtools

Read merging

PEAR
BBtools

Gene prediction

FragGeneScan
Prodigal

Read Mapping

Bowtie2 Samtools

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 on the ENA Web Page. Please consider the different download options e.g. by reading ENA documentation. What other options are available? Which one is the best?