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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
thanks
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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.Comment
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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), ...Comment
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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).Originally posted by steven View Post
Just a thought :-)Comment
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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 KumarComment
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Yes, that would be correct. Trim the qual score too.Originally posted by parveendabas View PostComment
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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.Comment
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thank you... cheers.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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