iarcbioinfo/alignment-nf repository overview

⁠alignment-nf

⁠Nextflow pipeline for BAM realignment or fastq alignment

⁠Description

Nextflow pipeline to perform BAM realignment or fastq alignment and QC, with/without local indel realignment and base quality score recalibration.

⁠Dependencies

1. Nextflow : for common installation procedures see the IARC-nf⁠ repository.

⁠Basic fastq alignment

1. bwa2⁠ (default) or bwa⁠
2. samblaster⁠
3. sambamba⁠

⁠BAM files realignment

1. samtools⁠

⁠Adapter sequence trimming

1. AdapterRemoval⁠

⁠ALT contigs handling

1. the k8 javascript execution shell (e.g., available in the bwakit⁠ archive); must be in the PATH
2. javascript bwa-postalt.js and the additional fasta reference .alt file from bwakit⁠ must be in the same directory as the reference genome file.

⁠QC

1. Qualimap⁠.
2. Multiqc⁠.

⁠Base quality score recalibration

1. GATK4⁠; wrapper 'gatk' must be in the path
2. GATK bundle⁠ VCF files with lists of indels and SNVs (recommended: Mills gold standard indels VCFs, dbsnp VCF), and corresponding tabix indexes (.tbi)

A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")

⁠Input

⁠Parameters

• ⁠Mandatory

• ⁠Optional

• ⁠Flags

Flags are special parameters without value.

⁠Usage

To run the pipeline on a series of fastq or BAM files in folder input and a fasta reference file hg19.fasta, one can type:

nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity  --input_folder input/ --ref hg19.fasta --output_folder output

To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

⁠Use bwa-mem instead of bwa-mem2

To use bwa-mem, one can type:

nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity  --input_folder input/ --ref hg19.fasta --output_folder output --bwa_mem "bwa mem"

⁠Enable adapter trimming

To use the adapter trimming step, you must add the --trim option, as well as satisfy the requirements above mentionned. For example:

nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity  --input_folder input/ --ref hg19.fasta --output_folder output --trim

⁠Enable ALT mode

To use the alternative contigs handling mode, you must provide the path to an ALT aware genome reference (e.g., hg38) AND add the --alt option, as well as satisfy the above-mentionned requirements. For example:

nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity  --input_folder input/ --ref hg19.fasta --output_folder output --postaltjs /user/bin/bwa-0.7.15/bwakit/bwa-postalt.js --alt

⁠Enable base quality score recalibration

To use the base quality score recalibration step, you must provide the path to 2 GATK bundle VCF files with lists of known snps and indels, respectively, AND add the --recalibration option, as well as satisfy the requirements above mentionned. For example:

nextflow run iarcbioinfo/alignment-nf -r v1.3 -profile singularity  --input_folder input/ --ref hg19.fasta --output_folder output --snp_vcf GATKbundle/dbsnp.vcf.gz --indel_vcf GATKbundle/Mills_1000G_indels.vcf.gz --recalibration

⁠Output

⁠Directed Acyclic Graph

⁠FAQ

⁠Why did Indel realignment disappear from version 1.0?

Indel realignment was removed following new GATK best practices for pre-processing.

⁠Contributions