FastUniq - De Novo Duplicates Removal Tool

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FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads ¹:

• Eliminates PCR-introduced duplicates, improving the accuracy of genome assembly and variation discovery.
• Processes paired-end reads without requiring a reference genome, ideal for de novo sequencing.
• A command-line tool that is straightforward to use for preprocessing sequencing data.
• Ultra-fast : Handles 87 million reads in 10 minutes ¹, ensuring rapid preprocessing of sequencing data.
• Free to download and use; A command-line tool and application that is straightforward to use for preprocessing sequencing data.

FastUniq Installation Guide

Install using Source Code

1. Download the Source Code:
   FastUniq can be downloaded from Source Forge repository or via wget command. This guide is for linux system (ubuntu) or WSL on windows:

Dependencies: Make sure the gcc compiler installed on your computer (Version 4.0 or above)

   wget https://sourceforge.net/projects/fastuniq/files/latest/download 

1. Extract the Package:
   Extract the downloaded archive:

   tar -xvzf FastUniq.tar.gz
   

2. Navigate to the Directory:
   Move to the extracted FastUniq directory:

   cd FastUniq
   

3. Compile the Tool:
   Compile the source code using make:

   make
   

4. Verify Installation:
   After compilation, the fastuniq binary will be created in the directory. Check the installation by running:

   ./fastuniq
   

5. Optional - Add to PATH:
   To use FastUniq globally, move the binary to a directory in your system’s PATH or add its directory to the PATH:

   sudo mv fastuniq /usr/local/bin/
   

   Or update your PATH:

   export PATH=$PATH:/path/to/FastUniq
   

conda install

To install this package run one of the following:

```bash
conda install bioconda::fastuniq
# OR you can use
conda install bioconda/label/cf201901::fastuniq
```

Parameters of FastUniq

1. -i: Input File List
   • Specifies a list of paired FASTQ sequence files as input. Two adjacent files with reads in the same order are treated as a pair.
   • Input: [FILE IN]
   • Limit: Maximum of 1000 pairs.
2. -t: Output Sequence Format
   • Defines the format of the output sequence files.
   • Options:
     • q: Outputs paired reads in FASTQ format into two separate files (default).
     • f: Outputs paired reads in FASTA format into two separate files.
     • p: Outputs paired reads in FASTA format into a single file (adjacent reads belong to the same pair).
3. -o: First Output File
   • Specifies the name of the first output file.
   • Input: [FILE OUT]
4. -p: Second Output File
   • Specifies the name of the second output file.
   • Input: [FILE OUT]
   • Note: Required only when the output format (-t) is q or f.
5. -c: Sequence Description Type
   • Determines how sequence descriptions are handled in the output files.
   • Options:
     • 0: Retains raw descriptions from input files (default).
     • 1: Assigns new serial numbers to descriptions.

Usage Example

For deduplicating paired-end FASTQ files and outputting in FASTQ format:

# Sample input_file_list.txt
reads_R1.fastq
reads_R2.fastq

# Command
fastuniq -i input_file_list.txt -t q -o clean_R1.fastq -p clean_R2.fastq

For deduplicating and outputting in single FASTA file:

fastuniq -i input_file_list.txt -t p -o output.fasta

Applications and Use Cases

1. Genome Assembly: Removing duplicates improves scaffolding and assembly accuracy.
2. Variant Calling: Ensures accurate detection of SNPs and other variations.
3. RNA-Seq Analysis: Reduces noise caused by duplicates for reliable expression analysis.
4. Metagenomics: Handles diverse datasets without a reference genome.

Reference

1. Xu H, Luo X, Qian J, Pang X, Song J, et al. (2012) FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads. PLOS ONE 7(12): e52249. https://doi.org/10.1371/journal.pone.0052249 ↩︎ ↩︎²