multi_k_velvet.sh

#multi k velvet

seq_file=$1

fq=$(basename $seq_file .trimmed.fq.keep.abundfilt)
for k in {19..51..2};
do
    quicksubmit "velveth && velvetg"

name=$(basename $i .pe.fq.gz);
pefile=$name.pe.fq.gz
sefile=$name.se.fq.gz;
for k in {19..51..2};
do
    echo "velveth $name.velvet.$k.d $k -fastq.gz -shortPaired $pefile -short $sefile && \
    velvetg $name.velvet.$k.d -exp_cov auto -cov_cutoff auto"
done