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aavf-spec

This repository defines the Amino Acid Variant Format, developed by the Winnipeg Consensus

accsense-scrape

Download alarm history from temperature sensors

aligntools

A Python library for manipulation of CIGAR, MSA, and other alignment formats.

bblab-server

Useful tools for HIV research from the Brockman and Brumme Lab at SFU

beast1-docker

Docker file for building old beast and beagle

best-prob-hla-imputation

Get the best probabilities from an HLA imputation

blind-dating

Data and manuscript for project on phylogenetic dating of HIV latency

cfe-lab.github.io

at the BC Centre for Excellence in HIV/AIDS

cfeintact

A bioinformatics tool for detecting defects in HIV-1 proviral sequences.

codon-by-codon

Codon by codon analysis

django-mock-queries

A library for mocking django queryset functions in memory for testing

fasta-converter

Converts FASTA to CSV and CSV to FASTA

genetracks

Generate track diagrams for genomic alignments

gotoh

Simple sequence aligner with high-level language bindings.

guava-layout

hcv_genotyper

hcvdb

Extract amino acid frequencies from hepatitis C virus GenBank records in H77 coordinate system

hiv-genome

HIV-I HXB2 Genome

hivintact

A proviral intactness pipeline.

hivseqinr

R-based pipeline that processes HIV near-full-genome sequences and classifies genomes into "intact" or into various "defective" categories.

hla-class

HLA class I sequence-based typing

hyphy-python

iva

de novo virus assembler of Illumina paired reads

kive

Archival and automation of bioinformatic pipelines and data

kive-default-docker

Docker file for building MiCall execution environment to run under Kive

make_tree

Simple script for drawing phylogenetic trees

micall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

micall_accessories

Some accessory scripts I created to do one-off tasks

miseqqcreport

Quality control report for the MiSeq.

mixed-hcv

Detected mixed genotype HCV infections by mapping short read data to reference genomes