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Post alignement

Image PostAlign

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

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