/baseseq

baseseq - Tool to generate haplotypes from BAsE-Seq libraries

Primary LanguagePython

baseseq - Tool to generate haplotypes from BAsE-Seq libraries

Acknowledgement

Hong et. al. - BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads

Summary

This is an unofficial repository of scripts used to analyze viral HBV reads generated from the BAsE-Seq protocol.

Prerequisite Dependencies

Python Libraries

  • pysam
  • CrossMap

Usage

  1. Run Analysis
python2.7 baseseq.py baseseq <options>
  -b --bam <bam>
  -r --ref <reference>
  -a --barcodes <barcodes>
  -p --out-prefix </path/to/prefix>
  -c --crossmap-bin </path/to/dir>
  -h --help

Output Files

  • vcf (.vcf)
  • consensus genome (.consensus.fa)
  • demultiplexed consensus for individual genomes (.cg.fa)
  • haplotype frequency (.freq)
  • summary statistics (.out)
  • UCSC chain file between reference and consensus genome (.chain)
  • barcodes (.txt)