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