Hong et. al. - BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads
This is an unofficial repository of scripts used to analyze viral HBV reads generated from the BAsE-Seq protocol.
Python Libraries
- pysam
- CrossMap
- 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
- 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)