bioRxivBioinformaticsPreprint
benchNGS : An approach to benchmark short reads alignment tools
Farzana Rahman, Mehedi HassaniD, Alona Martin Kryshchenko, Inna Dubchak, Nikolai Nickolai Alexandrov, Tatiana TatarinovaiD
Abstract
In the last decade a number of algorithms and associated software were developed to align next generation sequencing (NGS) reads to relevant reference genomes. The results of these programs may vary significantly, especially when the NGS reads are contain mutations not found in the reference genome. Yet there is no standard way to compare these programs and assess their biological relevance.\n\nWe propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. In this paper we outline the method and also present a short report of an experiment performed on five popular alignment tools.
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Accuracy, speed and error tolerance of short DNA sequence aligners
Mark Ziemann·bioRxiv·May 16, 2016
- Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li, Richard Michael Durbin·BioinformaticsPeer-reviewed·May 18, 2009
- Minimap2: pairwise alignment for nucleotide sequences
Heng Li·BioinformaticsPeer-reviewed·May 4, 2018
- BURST enables mathematically optimal short-read alignment for big data
Gabriel A. Al‐Ghalith, Dan Knights·bioRxiv·Sep 8, 2020
- Fast and accurate short read alignment with hybrid hash-tree data structure
Junichiro Makino, Toshikazu Ebisuzaki, … Yoshihide Hayashizaki·Genomics & InformaticsPeer-reviewed·Oct 29, 2024
- Alignathon: A competitive assessment of whole genome alignment methods.
Dent Earl, Ngan K Nguyen, … Benedict Paten·Genome ResearchPeer-reviewed·Oct 1, 2014