FastX
FastX is a software for sequence analysis and data quality control. It can process FASTA and FASTQ files to trim sequences, filter reads by quality or length, collapse or expand paired-end reads, and convert between formats.
sequence-analysis
quality-control
fasta
fastq
FastX: Sequence Analysis & Data Quality Control Software
Process FASTA and FASTQ files for sequence analysis and data quality control with FastX, a powerful software tool that offers features like sequence trimming, read filtering, paired-end handling, and format conversion.
What is FastX?
FastX is an open-source command line tool for basic sequence analysis and processing of FASTA and FASTQ files. It allows users to perform common data preparation and quality control tasks such as:
- Trimming low quality bases from read ends
- Filtering reads by length or quality score thresholds
- Collapsing or expanding paired-end reads
- Converting between FASTQ and FASTA formats
- Getting basic statistics about the reads
FastX is very fast and memory efficient, making it suitable for processing large NGS datasets. It utilizes multiple CPU cores for parallel processing to maximize throughput. The command line interface provides flexibility to build custom analysis pipelines by combining various FastX commands. The simplicity and speed of FastX has made it one of the most widely used tools for initial raw read processing and QC.
Some key advantages of FastX are:
- Very fast - processes millions of reads per minute
- Low memory footprint
- Multi-threaded to use multiple CPU cores
- Flexible command line interface
- Trusted quality and speed by many sequencing centers
Overall, FastX provides a set of simple building blocks to filter, trim, convert and analyze sequence reads that can be easily integrated into any bioinformatics workflow.
FastX Features
Features
- Quality trimming
- Adapter trimming
- Quality filtering
- Length filtering
- Paired-end read collapsing
- Paired-end read expansion
- FASTA/FASTQ format conversion
Pricing
- Open Source
Pros
Fast processing speed
Support for multi-threaded parallel processing
Flexible quality and length filtering options
Collapsing and expansion of paired-end reads
Free and open source
Cons
Limited analysis functions compared to larger NGS suites
Minimal graphical user interface
Primarily command line driven
Lacks support for some advanced file formats
Official Links
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