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.

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

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