Antibody NGS Pipeline

Bulk antibody sequence preprocessing, annotation with abstar, import to MongoDB.
This is based on the AbStar analysis pipeline: (www.github.com/briney/abstar)

install

pip install antibody-ngs-pipeline

use

To run antibody_ngs_pipeline:
antibody_ngs_pipeline

To run antibody_ngs_pipeline with FASTQC report on raw data:
antibody_ngs_pipeline -f

To run antibody_ngs_pipeline with adapter trimming by CutAdapt:
antibody_ngs_pipeline -t <path-to-adapters.fasta>

To run antibody_ngs_pipeline with quality trimming by sickle:
antibody_ngs_pipeline -q

To run antibody_ngs_pipeline with adapter trimming by CutAdapt, quality trimming with sickle and get a FASTQC report on both raw data and processed data:
antibody_ngs_pipeline -f -q -t <path-to-adapters.fasta>

requirements

Python 3.5+
abstar
abutils
cutadapt
pymongo

Downloading from BaseSpace requires Basemount: https://basemount.basespace.illumina.com/
Quality trimming requires sickle: https://github.com/najoshi/sickle
FastQC report requires FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Merging paired sequences requires PANDAseq: https://github.com/neufeld/pandaseq
batch_mongoimport (from Abstar) requires MongoDB: http://www.mongodb.org/