Installing FASTX Toolkit

Not sure how I got away so long without FASTX toolkit on my iMac. Followed these install instructions to get it set up on my computer (need to quality trim the 18S chimera sequences):

First, libgtextutils:

curl -O
tar xvjf libgtextutils-0.6.tar.bz2
cd libgtextutils-0.6
sudo make install

Then the FASTX-Toolkit – note the step to define PKG_CONFIG_PATH:

curl -O
tar xjvf fastx_toolkit-0.0.13.tar.bz2
cd fastx_toolkit-0.0.13
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
sudo make install

Then I used fastq_quality_filter to remove low quality reads:

fastq_quality_filter -i chim_demux.extendedFrags_primersremoved.fastq -o chim_demux.extendedFrags_primersremoved_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20
Minimum percentage: 80
Input: 2829756 reads.
Output: 2746576 reads.
discarded 83180 (2%) low-quality reads.

This site has a good tutorial for using FASTX trim to quality filter reads. And this site is where I got the install help for the FASTX toolkit.

Next step was to convert FASTQ to FASTA:

fastq_to_fasta -i chim_demux.extendedFrags_primersremoved_fastxtrimmed.fastq -o chim_demux.extendedFrags_primersremoved_fastxtrimmed.fasta -n -v -Q 33

Input: 2746576 reads.
Output: 2746576 reads.

I was originally getting an “invalid quality score value” error, but upon further investigation it seems like you need to use the -Q 33 parameter to indicate the new encoding on Illumina quality values (see here:


4 Responses to Installing FASTX Toolkit

  1. Bede says:

    I was relieved to find your post, but this isn’t working for me on 10.9. ‘No makefile found’ on trying to make fastx-toolkit. Any ideas? Thanks

    • hollybik says:

      I think I was running into a similar problem recently when I tried this install on my new MacBookPro laptop – I gave up (it wasn’t urgent) and never found a fix, so let me know if you find a solution. Will update this thread when I try the fasts toolkit install again.

  2. Rehan says:

    Installation worked perfectly well on OS 10.8.5. Thank you for saving my time.

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