Quality trimmming / Mask low quality bases?

[bbimber]

Does anyone know of a command line utility that can accept either FASTA/QUAL or FASTQ files and mask any bases below a given quality score (ie. convert them to N)?

Does anyone have suggestions on the best utilities to perform quality score based end trimming?

Thank you for any help or suggestions.

[maubp]

Most people I've talked to use their own Perl or Python scripts for this, although EMBOSS are looking at adding this kind of tool to their suite.

[bbimber]

ok, thanks for the reply. that's the impression I was getting from google.

in case anyone else reads this, i did come across this:

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

[bioenvisage]

hi .. is there any script to mask or remove the low quality repeats and also simple repeats..I would also
like to know whether this will create problems in denovo assembly...

[Zigster]

ok, thanks for the reply. that's the impression I
http://hannonlab.cshl.edu/fastx_toolkit/index.html

is the FASTQ Quality Filter a variable trimmer?

[gabriel.lichtenstein]

updates on this thread?

would you suggest me a perl script for quality trimming illumina 1.3 reads?

what do you think about clc trim sequences tool? and abyss -q option?

[maubp]

I don't have any perl examples, but there are some very simple Python examples in the Biopython Tutorial (search for FASTQ):

http://biopython.org/DIST/docs/tutorial/Tutorial.html

http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

and here:

http://news.open-bio.org/news/2009/09/biopython-fast-fastq/

[Simon Anders]

I am unconvinced that trimming low quality reads is necessary at all. After all, most aligners (e.g., Maq, Bowtie, BWA; but not Eland!) take into account the quality score and disregard or downweight low quality reads automatically.

Simon

[bbimber]

if you are interested in illumina, look into fastx toolkit (link above). there's a command line tool to do it. they might also have a web interface for it, but i'm not 100% positive. the logic behind their trimming is probably good for short reads, but not as optimal for longer ones like 454.

[xuer]

Yes it tells you the number of reads that have been marked as duplicates, as well as the total number of reads. But note that reads that Picard marks as duplicates do not necessarily have identical sequence they just map to the same chromosomal location.

so , it looks that Picard is not good choice for that