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

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# 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/

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