Read clustering using VSEARCH

Author

Menachem Sklarz

Affiliation

Bioinformatics Core Facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

This workflow demonstrates methods to cluster reads with the vsearch module.

Steps:

  1. fastq files are dereplicated with vsearch at the sample scope (vsearch produces a `fasta` file),

  2. resulting unique sequences are merged to obtain a project-level fasta file,

  3. project level fasta file is again dereplicated and

  4. resulting sequences are clustered using vsearch and cd-hit (the user can choose between them)

Workflow Schema

Read clustering DAG

Requires

  • fastq files, either paired-end or single-end.

Programs required

Example of Sample File

Title       ChIP_project

#SampleID   Type    Path    lane
Sample1     Forward /path/to/Sample1_F1.fastq.gz 1
Sample1     Forward /path/to/Sample1_F2.fastq.gz 2
Sample1     Reverse /path/to/Sample1_R1.fastq.gz 1
Sample1     Reverse /path/to/Sample1_R2.fastq.gz 2
Sample2     Forward /path/to/Sample2_F1.fastq.gz 1
Sample2     Reverse /path/to/Sample2_R1.fastq.gz 1
Sample2     Forward /path/to/Sample2_F2.fastq.gz 2
Sample2     Reverse /path/to/Sample2_R2.fastq.gz 2

Download

The workflow file is available here