Fastp - A fast all-in-one FASTQ preprocessor with QC, adapter trimming and quality filtering

Fastp is a tool designed to provide a fast and comprehensive solution for pre-processing high-throughput sequencing data in FASTQ format. It performs quality control, adapter trimming, and quality filtering all in one go.

Fastp is written in C++ and is highly optimized to run on both CPU and memory-efficient hardware. It has been tested on Linux, macOS, and Windows.

Features

• Fast and memory-efficient processing of large-scale sequencing data
• Adapter trimming (support for both single-end and paired-end data)
• Quality control and filtering based on Phred scores
• PolyG/C trimming
• Length filtering
• Reporting in HTML, JSON or CSV format
• Multi-threading

Installation

Fastp can be easily installed using the conda package manager:

conda install -c bioconda fastp

Alternatively, you can clone the Fastp GitHub repository and compile it from source:

git clone https://github.com/OpenGene/fastp.git
cd fastp
make

Usage

Fastp is very easy to use. Here's an example command for processing a pair of paired-end data files:

fastp -i R1.fq.gz -I R2.fq.gz -o R1_trimmed.fq.gz -O R2_trimmed.fq.gz

This command assumes that your data files are in Gzipped FASTQ format. You can specify any of the supported input and output formats using the -f and -F flags. For a full list of options and usage examples, see the official Fastp user guide.

Contributions

Fastp is an open-source project that welcomes contributions from the community. If you have found a bug, have a feature request, or have fixed a bug, please submit an issue or pull request on GitHub.

Conclusion

If you're looking for a fast, memory-efficient, and comprehensive all-in-one FASTQ preprocessor, Fastp is definitely worth checking out. It's easy to install, easy to use, and comes with all the features you need to get your sequencing data ready for downstream analysis.

Markdown

# Fastp - A fast all-in-one FASTQ preprocessor with QC, adapter trimming and quality filtering

![Fastp logo](https://raw.githubusercontent.com/OpenGene/fastp/master/fastp_logo.png)

Fastp is a tool designed to provide a fast and comprehensive solution for pre-processing high-throughput sequencing data in FASTQ format. It performs quality control, adapter trimming, and quality filtering all in one go. 

Fastp is written in C++ and is highly optimized to run on both CPU and memory-efficient hardware. It has been tested on Linux, macOS, and Windows. 

## Features

* Fast and memory-efficient processing of large-scale sequencing data
* Adapter trimming (support for both single-end and paired-end data)
* Quality control and filtering based on Phred scores
* PolyG/C trimming
* Length filtering
* Reporting in HTML, JSON or CSV format
* Multi-threading

## Installation

Fastp can be easily installed using the `conda` package manager:

```bash
conda install -c bioconda fastp

Alternatively, you can clone the Fastp GitHub repository and compile it from source:

git clone https://github.com/OpenGene/fastp.git
cd fastp
make

Usage

Fastp is very easy to use. Here's an example command for processing a pair of paired-end data files:

fastp -i R1.fq.gz -I R2.fq.gz -o R1_trimmed.fq.gz -O R2_trimmed.fq.gz

This command assumes that your data files are in Gzipped FASTQ format. You can specify any of the supported input and output formats using the -f and -F flags. For a full list of options and usage examples, see the official Fastp user guide.

Contributions

Fastp is an open-source project that welcomes contributions from the community. If you have found a bug, have a feature request, or have fixed a bug, please submit an issue or pull request on GitHub.

Conclusion

If you're looking for a fast, memory-efficient, and comprehensive all-in-one FASTQ preprocessor, Fastp is definitely worth checking out. It's easy to install, easy to use, and comes with all the features you need to get your sequencing data ready for downstream analysis.