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Assembly with metaSPAdes

Here are the instructions for assembling the metagenomic data with a different assembler. Here we are showing metaSPAdes, one of the assembler options highlighted in the CAMI paper.

metaSPAdes takes longer than MEGAHIT to run the assembly, so we will not be running it during the course. Rather it is available for download here. If you are interested in running the assembly yourself, however, please see below.

Install metaSPAdes:

wget http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1-Linux.tar.gz
tar -xzf SPAdes-3.10.1-Linux.tar.gz
export PATH=$PATH:~/SPAdes-3.10.1-Linux/bin/

Concatenate the two sets of reads:

cd ~/data
for x in *gz
do
  gunzip $x
done

cat *fq > coassembly.fq

cd ~
mkdir assembly-spades
cd assembly-spades

And assemble with metaSPAdes:

metaspades.py --12 ~/data/coassembly.fq -o metaS-assembly