2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2021

Susana Posada-Cespedes, David Seifert, Ivan Topolsky, Kim Philipp Jablonski, Karin J. Metzner, Niko Beerenwinkel. V-pipe: a computational pipeline for assessing viral genetic diversity fromhigh-throughput data. Bioinformatics, 2021.

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MOTIVATION: High-throughput sequencing technologies are used increasingly, not
only in viral genomics research but also in clinical surveillance and
diagnostics. These technologies facilitate the assessment of the genetic
diversity in intra-host virus populations, which affects transmission, virulence,
and pathogenesis of viral infections. However, there are two major challenges in 
analysing viral diversity. First, amplification and sequencing errors confound
the identification of true biological variants, and second, the large data
volumes represent computational limitations. RESULTS: To support viral
high-throughput sequencing studies, we developed V-pipe, a bioinformatics
pipeline combining various state-of-the-art statistical models and computational 
tools for automated end-to-end analyses of raw sequencing reads. V-pipe supports 
quality control, read mapping and alignment, low-frequency mutation calling, and 
inference of viral haplotypes. For generating high-quality read alignments, we
developed a novel method, called ngshmmalign, based on profile hidden Markov
models and tailored to small and highly diverse viral genomes. V-pipe also
includes benchmarking functionality providing a standardized environment for
comparative evaluations of different pipeline configurations. We demonstrate this
capability by assessing the impact of three different read aligners (Bowtie 2,
BWA MEM, ngshmmalign) and two different variant callers (LoFreq, ShoRAH) on the
performance of calling single-nucleotide variants in intra-host virus
populations. V-pipe supports various pipeline configurations and is implemented
in a modular fashion to facilitate adaptations to the continuously changing
technology landscape. AVAILABILITY: V-pipe is freely available at
https://github.com/cbg-ethz/V-pipe. SUPPLEMENTARY INFORMATION: Supplementary data
are available at Bioinformatics online.