how to correct list of many long reads files for Proovread?

Question

[xiachongjing]

Hello:

Anyone familiar with software Proovread? I got some problem.

After I got ~100 .fq long reads files from SeqChunker step (as suggested by the program mannual), I wonder how to add this list of files into the program? for example, we can use <-s 1.fq -s 2.fq -s 3.fq> for many high quality short reads, how to deal with ~100 long reads .fq files.

In the proovread.cfg file, it says (line37-38):

LIST of Pacbio read files to correct. FASTA or FASTQ format.

'long-reads' => [],

However, I cannot figure out how to use this option.

I tried:

'long-reads' => [pb-001.fq],[pb-002.fq]

'long-reads' => [pb-001.fq], 'long-reads' => [pb-002.fq],

'long-reads' => [*.fq],

ALL of them are FAILED. Any suggestions? Thanks

Answer 1

[Medhat]

can you try this so it will loop through all files and print them

proovread -l pb-001.fq `for i in *.fq; do echo "-s $i" | tr "\n" " " ; done`