Code for Metagenomic assembly

Simon Rasmussen - June 2013

This is the code for running the de novo assembly of the MH0032 and MH0047 samples from the MetaHit experiment. We will assemble them using SOAPdenovo and MetaVelvet, first is the code for MH0032 using SOAPdenovo - the "-p 4" tells SOAPdenovo to use 4 cores in parallel and below is the code for MetaVelvet. We are using the k-mer 31 for both assemblies, but one could try different ones.

SOAPdenovo:

cp /home/local/27626/exercises/metagenomics/MH0032.soap.config .
SOAPdenovo-31mer all -K 31 -s MH0032.soap.config -p 4 -o MH0032_d0

MetaVelvet:

ln -s /home/local/27626/exercises/metagenomics/MH0032/081224/MH0032_081224.rmHuman.rmHost.1.fq.gz .
ln -s /home/local/27626/exercises/metagenomics/MH0032/081224/MH0032_081224.rmHuman.rmHost.2.fq.gz .
ln -s /home/local/27626/exercises/metagenomics/MH0032/090121/MH0032_090121.rmHuman.rmHost.1.fq.gz .
ln -s /home/local/27626/exercises/metagenomics/MH0032/090121/MH0032_090121.rmHuman.rmHost.2.fq.gz .

velveth MH0032_31 31 -shortPaired -fastq.gz -separate MH0032_081224.rmHuman.rmHost.1.fq.gz MH0032_081224.rmHuman.rmHost.2.fq.gz \
-shortPaired2 -fastq.gz -separate MH0032_090121.rmHuman.rmHost.1.fq.gz MH0032_090121.rmHuman.rmHost.2.fq.gz
velvetg MH0032_31 -exp_cov auto -read_trkg yes
meta-velvetg MH0032_31 -ins_length 127 -ins_length2 362 | tee logfile

SOAPdenovo:

cp /home/local/27626/exercises/metagenomics/MH0047.soap.config .
SOAPdenovo-31mer all -K 31 -s MH0047.soap.config -p 4 -o MH0047_d0

MetaVelvet:

ln -s /home/local/27626/exercises/metagenomics/MH0047/081223/MH0047_081223.rmHuman.rmHost.1.fq.gz .
ln -s /home/local/27626/exercises/metagenomics/MH0047/081223/MH0047_081223.rmHuman.rmHost.2.fq.gz .
ln -s /home/local/27626/exercises/metagenomics/MH0047/090201/MH0047_090201.rmHuman.rmHost.1.fq.gz .
ln -s /home/local/27626/exercises/metagenomics/MH0047/090201/MH0047_090201.rmHuman.rmHost.2.fq.gz .

velveth MH0047_31 31 -shortPaired -fastq.gz -separate MH0047_081223.rmHuman.rmHost.1.fq.gz MH0047_081223.rmHuman.rmHost.2.fq.gz \
-shortPaired2 -fastq.gz -separate MH0047_090201.rmHuman.rmHost.1.fq.gz MH0047_090201.rmHuman.rmHost.2.fq.gz
velvetg MH0047_31 -exp_cov auto -read_trkg yes
meta-velvetg MH0047_31 -ins_length 127 -ins_length2 362 | tee logfile