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NeatSeq-Flow Tutorial Workflow

Author

Menachem Sklarz and Liron Levin

Affiliation

Bioinformatics Core Facility

Organization

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

Module categories

This tutorial describes how to create and execute the workflow described in the NeatSeq-Flow manuscript (Article on BioRXiv).

See NeatSeq-Flow Tutorial for detailed instructions for quick installation of the tutorial workflow with conda.

The example workflow receives FASTQ files and the sequenced genome of a bacteria. It then performs:

  • Quality testing and trimming of the raw sequence reads (paired- or single-end).
  • Alignment (“mapping”) of the reads to a reference genome using two different programs.
  • Sorting the samples' BAM files as final results.
  • Creation of a report on reads and mapping quality.

Workflow Schema

Example Workflow DAG

Steps

Step Module Program
Merge merge -
Fastqc_Merge fastqc_html fastqc
Trimmomatic trimmo trimmomatic
FastQC_Trimmomatic fastqc_html fastqc
BWA_Index_Builder bwa_builder bwa
BWA bwa_mapper bwa
Bwt2_Index_Builder bowtie2_builder bowtie2
Bwt2 bowtie2_mapper bowtie2
Samtools_BWA samtools samtools
Samtools_Bwt2 samtools samtools
QC_and_Map_MultQC Multiqc MultiQC

Required data

This WF requires samples with fastq file(s) (paired or single) and a reference genome in fasta format.

Programs required

  • fastqc
  • trimmomatic
  • multiqc
  • samtools=1.3
  • BWA
  • bowtie2

Example of Sample File

Title    Example_WF_From_the_manuscript

#Type    Path
Nucleotide   /path/to/Reference_genome.fasta

#SampleID    Type    Path
Sample1  Forward /path/to/Sample1.F.fastq.gz
Sample1  Reverse /path/to/Sample1.R.fastq.gz
Sample2  Forward /path/to/Sample2.F.fastq.gz
Sample2  Reverse /path/to/Sample2.R.fastq.gz
Sample3  Forward /path/to/Sample3.F.fastq.gz
Sample3  Reverse /path/to/Sample3.R.fastq.gz

Download

curl -LO https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-tutorial/master/Samples_conda.nsfs

curl -LO https://raw.githubusercontent.com/bioinfo-core-BGU/neatseq-flow-tutorial/master/Example_WF_conda_env.yaml