https://github.com/cihga39871/atria

An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
https://github.com/cihga39871/atria

illumina ngs paired-end quality trim-adapters trimmer trimming

Last synced: 3 months ago
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An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.

• Host: GitHub
• URL: https://github.com/cihga39871/atria
• Owner: cihga39871
• License: other
• Created: 2020-09-05T14:52:52.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2025-02-25T17:19:17.000Z (3 months ago)
• Last Synced: 2025-02-25T18:29:08.139Z (3 months ago)
• Topics: illumina, ngs, paired-end, quality, trim-adapters, trimmer, trimming
• Language: Julia
• Homepage:
• Size: 2 MB
• Stars: 35
• Watchers: 2
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE.md

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README

        
# Atria

![](https://img.shields.io/github/downloads/cihga39871/Atria/total)

 

Atria is designed to trim adapters and low-quality bases of next-generation sequencing data. It infers the insert DNA precisely by integrating both adapter information and reverse-complementary properties of pair-end reads within a delicate decision tree. It can also remove duplicated sequences due to PCR amplification.

If you use Atria, please cite the paper:

> Jiacheng Chuan, Aiguo Zhou, Lawrence Richard Hale, Miao He, Xiang Li, Atria: an ultra-fast and accurate trimmer for adapter and quality trimming, Gigabyte, 1, 2021  https://doi.org/10.46471/gigabyte.31

## Features

- FAST, even for compressed fastqs

- Highly accurate Illumina adapter trimming

- Paired-end consensus calling

- Quality trimming

- Poly X tail trimming

- Hard clip 3' and 5' ends

- N tail trimming

- Filtering reads by the number of N bases

- Filtering reads by length

- Filtering reads by read complexity

- Remove PCR duplicates (dedup)

## Contents

1. Installation guide

   1.1 [Release installation guide](docs/1.1.Release_installation_guide.md)

   1.2 [Install from source](docs/1.2.Install_from_source.md)

2. **[Atria trimming methods and usages](docs/2.Atria_trimming_methods_and_usages.md)**

3. [Benchmark toolkit](docs/3.Benchmark_toolkit.md)

4. [Atria development notes](docs/4.Development_notes.md)

5. **[Accuracy and speed benchmark](docs/5.Accuracy_and_speed_benchmark.md)**