Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

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

Project description

# 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/

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for antibody-ngs-pipeline, version 1.0.3.dev0
Filename, size File type Python version Upload date Hashes
Filename, size antibody_ngs_pipeline-1.0.3.dev0-py3-none-any.whl (9.5 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size antibody_ngs_pipeline-1.0.3.dev0.tar.gz (6.5 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page