ecoli-first-pass.sh

for i in 2 7 8
do
    fastq-dump --split-files --defline-seq '@$ac.$si.$sg/$ri' --defline-qual '+' -Z --gzip SRR03025${i} \
        > SRR03025${i}.fq.gz
done

for i in 2 7 8
do
    trim-low-abund.py -k 17 -M 250M --variable-coverage -o SRR03025${i}.trim.fq.gz --gzip SRR03025${i}.fq.gz \
    2> SRR03025{}.trim.log &
done
wait

kevlar find \
    --controls SRR030252.trim.fq.gz \
    --ctrl_max 1 --case_min 8 --ksize 19 \
    --memory 250M --out ecoli.kevlar.txt \
    SRR03025[7,8].trim.fq.gz \
    2> ecoli.kevlar.find.log

kevlar collect \
    --memory 100M -k 19 --collapse \
    --out ecoli.kevlar.collect.tsv \
    ecoli.kevlar.txt \
    2> ecoli.kevlar.collect.log