Assembly with SPAdes and MEGAHIT

Requirements (from unbuntu 16.04 using filtered reads)

Disk space(60 gb) RAM(32 gb) Updated packages(see read filtering) Docker(see read filtering for installation instructions)

Link the data and run MEGAHIT

for filename in *.trim30.fq.gz
do 

    base=$(basename $filename .trim30.fq.gz)
    echo $base 

    docker run -v ${PWD}:/data -it quay.io/biocontainers/megahit:1.1.1--py36_0 \ 
    megahit --12 /data/${i} --out-prefix=${base} -o /data/${base}.megahit_output
done

Now run Quast to generate some assembly statistics

for file in *.megahit_output/*contigs.fa
do

    base=$(basename $file .contigs.fa)
    echo $base 

    docker run -v /${PWD}:/data -it quay.io/biocontainers/quast:4.5--boost1.61_1 \
    quast.py /data/${file} -o /data/${base}.megahit_quast_report
done

Link the data and run SPAdes

for filename in *pe.trim30.fq.gz
do
    base=$(basename $filename .trim30.fq.gz)
    echo $base

    docker run -v ${PWD}:/data -it quay.io/biocontainers/spades:3.10.1--py27_0 \
    metaspades.py --12 /data/${filename} \
    -o /data/${base}.spades_output
done 

Now run Quast to generate some assembly statistics

for file in *.spades_output
do 

    base=$(basename $file .spades_output)
    echo ${base}

    docker run -v ${PWD}:/data -it quay.io/biocontainers/quast:4.5--boost1.61_1 \
    quast.py /data/${base}.spades_output/contigs.fasta \
    -o data/${base}.spades_quast_report
done