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IntroductionThe FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
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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 specializedprograms. Example of such mapping programs are: Blat, SHRiMP,LastZ,MAQ and many many others.
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.
- FASTQ-to-FASTA converter
- FASTQ InformationChart Quality Statistics and Nucleotide Distribution
- FASTQ/A CollapserCollapsing identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)
- FASTQ/A TrimmerShortening reads in a FASTQ or FASTQ files (removing barcodes or noise).
- FASTQ/A Renamer
- FASTQ/A ClipperRemoving sequencing adapters / linkers
- FASTQ/A Reverse-ComplementProducing the Reverse-complement of each sequence in a FASTQ/FASTA file.
- FASTQ/A Barcode splitterSplitting a FASTQ/FASTA files containning multiple samples
- FASTA Formatterchanges the width of sequences line in a FASTA file
- FASTA Nucleotide Changer
- FASTQ Quality FilterFilters sequences based on quality
- FASTQ Quality Trimmer
- FASTQ MaskerMasks nucleotides with 'N' (or other character) based on quality
These tools can be used in two forms:
- Web-based (with Galaxy).
Galaxy's Test website already contains some of the FASTX-toolkit tools.
running the tools from command line (or as part of a script).
Tools demonstrationVisit the Hannon lab public galaxy server to see a demonstration of these (and other) tools.
02-Feb-2010 - Version 0.0.13New tools:
fastq_masker (suggested by Ben Bimber)
fastx_trimmer can trim N nucleotides from the end of the sequences (a new command line option, and a separate tool in Galaxy)
fastx_clipper accepts minimum adapter length to clip (requested by Erick Antezana, command line only)
Improved Galaxy integration:
Almost all tools have working functional tests (except the plotting tools and barcode splitter).
Plotting tools (nucleotide distribution and quality boxplot) detect input file type and show a detailed warning if given a FASTA/Q file as input
(hopefully reducing bug reports).
Tools read the input FASTQ type (sanger or solexa) and use the correct quality ASCII offset (33 for sanger, 64 for solexa).
Dec-2009 - Version 0.0.12never officially released
24-Nov-2009 - Version 0.0.11New tools: fastx_uncollapser, fastq_quality_filter.
New features: fastx_collapser can re-collapse an already-collapsed FASTA file; fastx_trimmer can trim N bases from the end of the sequence.
Minor compilation bug-fixes.
10-Aug-2009 - Version 0.0.10Bug fix on Mac OS X (reported by Joshua Waterfall).
New tool: FASTX-Renamer (based on suggestion+patch by Charles Plessy).
New undocumented command line argument: -Q NN handles FASTQ ASCII quality with user specified offset (was hard-coded as 64 in previous versions). Requested by Erick Antezana
Barcode-Splitter: improved galaxy integration - stores output files directly into galaxy's files database; no need for external webserver anymore.
Uses libgtextutils-0.5 library (as a dynamic library)
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Version 0.0.9Never released.
12-Mar-2009 - Version 0.0.8Minor changes to compilation stage, as suggested by users.
FASTX-toolkit should now compile cleanly on Mac OS x.
No new features were added.
Using libgtextutils-0.3 library.
24-Mar-2009 - Version 0.0.7Added Fasta-Formatter and Fasta-Nucleotide-Changer
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