antibody-ngs-pipeline 1.0.2.dev0

Bulk antibody sequence preprocessing, annotation with abstar, upload to MongoDB and S3

Antibody NGS Pipeline

Bulk antibody sequence preprocessing, annotation with abstar, upload to MongoDB and S3.
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/