AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Fuente:
arXiv
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Preprint |
| Published: |
2019
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866911640977408000 |
|---|---|
| author | Kim, Jeremie S. Firtina, Can Cavlak, Meryem Banu Cali, Damla Senol Alser, Mohammed Hajinazar, Nastaran Alkan, Can Mutlu, Onur |
| author_facet | Kim, Jeremie S. Firtina, Can Cavlak, Meryem Banu Cali, Damla Senol Alser, Mohammed Hajinazar, Nastaran Alkan, Can Mutlu, Onur |
| contents | AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4x. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants
AirLift source code and readme describing how to reproduce our results are available at https://github.com/CMU-SAFARI/AirLift. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_1912_08735 |
| institution | arXiv |
| publishDate | 2019 |
| record_format | arxiv |
| spellingShingle | AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes Kim, Jeremie S. Firtina, Can Cavlak, Meryem Banu Cali, Damla Senol Alser, Mohammed Hajinazar, Nastaran Alkan, Can Mutlu, Onur Genomics Computational Engineering, Finance, and Science AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run a downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4x. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants AirLift source code and readme describing how to reproduce our results are available at https://github.com/CMU-SAFARI/AirLift. |
| title | AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes |
| topic | Genomics Computational Engineering, Finance, and Science |
| url | https://arxiv.org/abs/1912.08735 |