Post alignement

Description

Perform a post alignement on aligned reads files.

Dependencies

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
2. samtools: see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)
3. sambamba : see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See theIARC-nf repository for more information.)
4. bwakit : see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)

Input

Name	Description
--input_folder	Folder containing Fasta files
--output_folder	Path to output folder

Parameters

Optional

Name	Example value	Description
samtools	/usr/bin/samtools	Path to samtools installation directory
sambamba	/usr/bin/sambamba	Path to sambamba installation directory
bwakit	/usr/bin/bwakit	Path to bwakit installation directory

Flags

Flags are special parameters without value.

Name	Description
--help	Display help

Download test data set

git clone https://github.com/iarcbioinfo/data_test

Usage

nextflow run WGS_analysis/PostAlign.nf --samtools /path/to/samtools --sambamba /path/to/sambamba --bwait /path/to/bwakit --input_folder path/to/input --output_folder /path/to/output

Output

Name	Description
Headers(*.HEAD)	First lines of the returned BAM file
BAMS(*.bam)	Improved alignment