Metadata-Version: 2.1
Name: antibody_ngs_pipeline
Version: 1.0.2.dev0
Summary: Bulk antibody sequence preprocessing, annotation with abstar, upload to MongoDB and S3
Home-page: https://www.github.com/CollinJ0/antibody_ngs_pipeline
Author: CollinJ0
License: UNKNOWN
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/  
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
