De novo Assembly followed by read mapping to the assembly using several mappers

Author

Menachem Sklarz

Affiliation

Bioinformatics Core Facility

Organization

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

This workflow demonstrates the use of the index building and mapping modules.

It creates an assembly and maps the reads to it.

Steps:

1. Merging (merge), quality testing (fastqc_html) and trimming (trimmo).

2. A sample-wise assembly is constructed with megahit.

3. Quality testing of the assembly with quast.

4. An index for the assembly is created with bowtie2_builder, bowtie_builder, bwa_builder and STAR_builder modules.

5. The reads are mapped to the assembly with bowtie2_mapper, bowtie_mapper, bwa_mapper and STAR_mapper modules.

Workflow Schema

Requires

fastq files. Either paired end or Single end.

Programs required

• megahit

• quast

• FastQC

• trimmomatic

• bowtie2

• bowtie

• bwa

• STAR

Example of Sample File

Title       Paired_end_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