Nextflow chip alignment

This nextflow pipeline is an attempt to align probes from a chip-manifest file on a reference genomes using blast. The reason of doing this is to define the strand orientation of the probe on the reference sequence, in order to be able to convert a genotype from illumina top to forward (or ALT/REF) coordinates. This pipeline was developed as a component of the SMARTER project (WP4 in particular) and will be the first step towards a new SNPchiMp release.

Requisites

To run this nextflow pipeline, you require both a genome reference sequence (better to download it from NCBI ftp) and a manifest csv file from an illumina/affymetrix chip. Next, you you will need nextflow installed and at least one of this different executors: conda, singularity and docker. You can choose to clone this repository if you plan to change this pipeline according your needs:

git clone https://github.com/cnr-ibba/nf-chip-alignment.git

The other way to running this pipeline is described in pipeline sharing nextflow manual.

Testing pipeline

You can test your local configuration by calling the test profile with one of the three supported executors. For example, to test this pipeline with singularity:

nextflow run cnr-ibba/nf-chip-alignment -resume -profile test,singularity

Running pipeline

You can call this pipeline with you local data using the --genome and --manifest options, for example:

nextflow run cnr-ibba/nf-chip-alignment -resume -profile singularity --manifest <manifest.csv> --genome <reference genome>

gzipped input files are supported.

About alignments

Alignments are made using megablast task, which is more stringent and faster then the default blastn. Alignments are filtered relying percentage aligned and percentage identity. A probe is considered unmapped if all alignments are filtered, if there are more than one alignment after filtering or if the SNP doesn't match to the reference genome. The last condition however is not correlated in a issue in alignment, however it could be difficult to join this particular SNP with other data or refer it to a reference SNP. For such reason SNP is discarded even if there's a perfect match of the probe