Filter out low coverage contigs

Question

[melissachua90]

I ran the Spades software (https://github.com/ablab/spades), which outputs contigs.fasta

for f in `ls -1 *_1.fq | sed 's/_1.fq//’`;
    do spades.py -o . --mismatch-correction -1 $f\_1.fq -2 $f\_2.fq -t 20;
done

Within the same directory, I created and executed a bash script filter_contigs.sh:

for file in contigs.fasta; do
        grep -F ">" $file | sed -e 's/_/ /g' |sort -nrk 6 |awk '$6>=2.0 && $4>=500 {print $0}'|
        sed -e 's/ /_/g'|sed -e 's/>//g'>$file.txt
        echo sequences to keep
        wc -l $file.txt
        echo running fastagrep.pl
        ../fastagrep.pl -f $file.txt $file > HCov.$file
        echo sequences kept
        grep -c ">" HCov.$file
done

When I executed filter_contigs.sh, it fails to capture/keep any contigs. Why?

sequences to keep
0 contigs.fasta.txt
running fastagrep.pl
sequences kept
0

[Pierre Lindenbaum]

what is the output of

grep -F ">" contigs.fasta

?

[melissachua90]

hmmm I didn't realize contigs.fasta is empty. Perhaps I will rerun spades. I think --mismatch-correction option is not available for my Spades' version.

[Mensur Dlakic]

Maybe --only-error-correction ?

[melissachua90]

I want to both correct and assemble the reads (I removed the previous error correction steps).

[Mensur Dlakic]

There is no switch needed for both error-correction and assembly, as that is a default behavior.

[melissachua90]

But if I use --only-error-correction, doesn't it mean that it won't perform the assembly? If I run spades.py -o . -1 read_1 -2 read_2 -t 20, it would perform both error correction and assembly, right?

[Joe]

A word of caution; it's been a while since I've used SPAdes so maybe this has changed but I'm pretty sure the "coverage" value in the header of SPAdes contigs is not sequence coverage, it is kmer coverage.