FASTX-TOOLKIT

This version of fastx_toolkit has been transferred to a modern version of Cmake, Perl scripts are temporally dropped from support.

Short Summary

The fastx_toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

More Details

Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).

The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs.

Example of such mapping programs are (many of them are unmaintained):

• Blat,
• SHRiMP,
• LastZ,
• MAQ
• And many many others.

However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results.

The fastx_toolkit tools perform some of these preprocessing tasks.

Available Tools

• fastq_to_fasta - Converts a FASTQ file to a FASTA file.

• fastx_quality_stats - scans a FASTQ file, and produces some statistics about the quality and the sequences in the file.

• fastq_quality_converter - Converts from ASCII to numeric quality scores.

• fastq_quality_filter - removes low-quality sequences from FASTQ files.

• fastx_artifacts_filter - removes some sequencing artifacts from FASTA/Q files.

• fastx_clipper - Adapters (aka Linkers) are added to the library (before sequencing), and should be removed from the resulting FASTA/Q file. This tool removes (clips) adapters.

• fastx_reverse_complement - Produces a reverse-complement of FASTA/Q file. If a FASTQ file is given, the quality scores are also reversed.

• fastx_trimmer - Extract sub-seqeunces from FASTA/Q file. Two examples are: Removing barcodes from the 5'-end of all sequences in a FASTQ file; Cutting 7 nucleotides from the 3'-end of all sequences in a FASTA file.

Other programs exist, but their description is not provided (yet)

• fastx_uncollapser - ?

• fastx_renamer - ?

• fastx_collapser - ?

• fastq_quality_trimmer - ?

• fasta_nucleotide_changer - ?

• fasta_formatter - ?

• seqalign_test - ?

Software Requirements

1. Cmake >= 3.15

2. GCC (passing on 13.2.0), but probably >= 6 will be sufficient

3. Pkg-config (passing on 0.29.2)

4. The libgtextutils package is required to build fasta_formatter and fastx_uncollapser tools, see this GitHub repository.

Installation

To install the tools one can do the following:

   $ git clone https://github.com/merv1n34k/fastx_toolkit
   $ cd fastx_toolkit
   $ mkdir build && cd build
   $ cmake ..
   $ make install

If you are on macOS (and probably Linux) you can use Homebrew:

   $ brew tap merv1n34k/tap
   $ brew install merv1n34k/tap/fastx_toolkit

Command Line Usage

Most tools support "-h" argument to show a short help screen. Better documentation is not available at this moment.

LICENSE

Distributed under the Affero GPL version 3 or later (AGPLv3), see LICENSE.

Notes from author

Assaf Gordon designed and implemented fastx_toolkit.

Many people have further contributed to fastx_toolkit by reporting problems, suggesting various improvements, or submitting actual code. Here is a list of these people. Help me keep it complete and exempt of errors.

Many Hannon-lab members at CSHL (who preferred to remain anonymous).

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Please send all comments, suggestions, bug reports (or better yet - bug fixes) to assafgordon@gmail.com.

Notes from me

Feel free to open issues in this repository, PRs are appreciated :3

Changes made

• Removed galaxy part of the fastx_toolkit
• Moved project from Autotools to Cmake
• Updated README
• Added Homebrew installation instruction