kantorlab / hivmmer

Alignment and variant-calling pipeline for Illumina HIV sequences.

kantorlab/hivmmer Issues

hivmmer fails on report generation
Updated 2 years ago2
How to use pre-packaged reference files with --ref
Updated 2 years ago
Does hivmmer accept fastq.gz files as input?
Updated 2 years ago
Instruction to build a pHMM reference
Updated 4 years ago
access to aavf file
Updated 4 years ago
Fix handling of deletions in consensus.py
Updated 4 years ago
Reference enquiry
Updated 4 years ago1
What should I be using as a reference?
Closed 5 years ago6
Add minimum coverage threshold when calling consensus sequence
Updated 5 years ago
improve consistency of whole genome coverage
Closed 5 years ago
Reimplement hivmmer wrapper in Python to support whole genome
Closed 5 years ago1
Include prepackaged pHMMs for whole genome
Closed 5 years ago
support for Gag?
Closed 5 years ago2
Validate hxb2 coordinates
Closed 5 years ago
Subtype C
Closed 5 years ago4
Determine optimal alignment score threshold
Closed 5 years ago
Report specific insertion codons
Closed 5 years ago
Add QC stage for filtering on quality score and read length
Closed 5 years ago