Entering edit mode
5.6 years ago
babdalhamid
•
0
Dear Sir/Madam:
I have the following script for spades, quast, and prokka. It is working perfect. However, there are several contigs with less than 200 in length. I need the minimum contig length 200. Spades manual does not say how to do it. Can you please help me with this?
#!/bin/bash
#SBATCH --time=7:00:00
#SBATCH --mem=200GB
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --workdir=/lustre/work/bahaabd/baha000/genomes_untrimmed_fastq/2018/group15
#SBATCH --job-name=group15
module load spades quast prokka python/2.7
combined_data=combined.quast.results.txt
while read r1 r2 output; do
spades.py -1 $r1 -2 $r2 -o $output
spades.py -1 $r1 -2 $r2 -o $output -t 4 --only-assembler
cd $output
quast.py contigs.fasta
prokka --genus Escherichia -usegenus contigs.fasta
cd ..
echo -e "$output\t$(tail -n 1 $output/quast_results/latest/transposed_report.tsv)" >> $combined_data
done < group15.txt
Thanks a lot. Baha
You can easily post-filter the contigs file to eliminate contigs smaller than 200bp.
I am a beginner in this field. I really do not know how to postfilter contigs. Would you please tell me how? Highly appreciate it. Baha
You can use a separate program. One recommendation
reformat.sh
from BBMap suite. You would do something like