Filtering and trimming data

[salmonella]

Is there a stand alone program (i.e. not incorporated into Velvet, Bowtie etc) that I can use to filter and trim Illumina fastq sequences

thanks

[malcook]

fastx toolkit

http://hannonlab.cshl.edu/fastx_toolkit/

[jameslz]

http://edwards.sdsu.edu/prinseq_beta/

[tnabtaf]

While not exactly standalone, there are a bunch filtering and QC options on the public Galaxy server. Go to usegalaxy.org and click on "NGS: QC and manipulation" in the left bar.

[mtmorgan]

R / Bioconductor has flexible tools in the ShortRead, Biostrings, and GenomicRanges packages. Some relevant functions include readFastq, writeFastq, SRFilter, trimLRPatterns, alphabet, alphabetByCycle, narrow, trimTails (in the `devel` branch), ...

[steven]

A new one: Btrim

[sklages]

A new one: Btrim

It would be helpful if these kind of tools would be aware of paired-ends and keep the final output file(s) synced (in terms of of read/mate positions/existence in output).
Just a thought :-)

[pd]

TRimming FASTQ file

Dear,

I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do i need to trim the line having qual score as well?

With REgards
Parveen Kumar

[Heisman]

Dear,

I want to trim my FASTq file (illumina) because of GT contamination in the beginning of every read. SO, my doubt is, When i trim the read sequence from 5' end (Left of the sequence) then do i need to trim the line having qual score as well?

With REgards
Parveen Kumar

Yes, that would be correct. Trim the qual score too.

[RockChalkJayhawk]

You should be able to trim reads directly, at least I know you can with Bowtie. Lok at the available options for all these tools.

[pd]

thank you... cheers.