AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
The PR adds several updates. Of note:
1) Runtime improvement around 4x (depending on copy number, coverage, etc)
2) Better filtering of arterfactual edges and intervals (alignment MAPQ, sequence entropy filters)
3) Handling of palindromic reads which can be confused with inverted reads.
4) Several bugfixes
5) Ability to specify reference using option --ref for amplified_intervals.py
The PR adds several updates. Of note: 1) Runtime improvement around 4x (depending on copy number, coverage, etc) 2) Better filtering of arterfactual edges and intervals (alignment MAPQ, sequence entropy filters) 3) Handling of palindromic reads which can be confused with inverted reads. 4) Several bugfixes 5) Ability to specify reference using option --ref for amplified_intervals.py