I am testing a metagenomic assembly pipline on a small E. coli data set provided by Sherine Awad and avaiable here

All raw Fastq sequences are in 'data/seqs/':

$find data/seq -name "*.fastq.gz"

After the sequencing data was downloaded our first step of analysis was assuring that the sequences are of high quality. We ran the sequence through a quality diagnostic and control pipeline:

1. Create base quality diagnostic graphs

Fastqc v 0.11.5

2. Trim poor quality bases

Trimmomatic or skewer

3. Assembly

MegaHIT

4. Assess assembly quality

Metaquast or

Followiing quality assesment reads were assemdbled using MEGAHIT v1.03

The assembly can be found in /metagenome_assembly/data/assembly/ecoli_ref-5m.megahit_assembly/