A brief history of bioinformatics
J Gauthier, AT Vincent, SJ Charette… - Briefings in …, 2019 - academic.oup.com
It is easy for today's students and researchers to believe that modern bioinformatics
emerged recently to assist next-generation sequencing data analysis. However, the very …
emerged recently to assist next-generation sequencing data analysis. However, the very …
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
ABSTRACT FASTQ has emerged as a common file format for sharing sequencing read data
combining both the sequence and an associated per base quality score, despite lacking any …
combining both the sequence and an associated per base quality score, despite lacking any …
[HTML][HTML] A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
Since its introduction in 2011 the variant call format (VCF) has been widely adopted for
processing DNA and RNA variants in practically all population studies—as well as in …
processing DNA and RNA variants in practically all population studies—as well as in …
[HTML][HTML] The ensembl variant effect predictor
W McLaren, L Gil, SE Hunt, HS Riat, GRS Ritchie… - Genome biology, 2016 - Springer
Abstract The Ensembl Variant Effect Predictor is a powerful toolset for the analysis,
annotation, and prioritization of genomic variants in coding and non-coding regions. It …
annotation, and prioritization of genomic variants in coding and non-coding regions. It …
[HTML][HTML] Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
The genus Oryza is a model system for the study of molecular evolution over time scales
ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the …
ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the …
[HTML][HTML] Efficient coalescent simulation and genealogical analysis for large sample sizes
J Kelleher, AM Etheridge… - PLoS computational …, 2016 - journals.plos.org
A central challenge in the analysis of genetic variation is to provide realistic genome
simulation across millions of samples. Present day coalescent simulations do not scale well …
simulation across millions of samples. Present day coalescent simulations do not scale well …
A general species delimitation method with applications to phylogenetic placements
Motivation: Sequence-based methods to delimit species are central to DNA taxonomy,
microbial community surveys and DNA metabarcoding studies. Current approaches either …
microbial community surveys and DNA metabarcoding studies. Current approaches either …
[HTML][HTML] Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus
Abstract The Southern Ocean houses a diverse and productive community of organisms,.
Unicellular eukaryotic diatoms are the main primary producers in this environment, where …
Unicellular eukaryotic diatoms are the main primary producers in this environment, where …
OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets
M Lohse, O Drechsel, S Kahlau… - Nucleic acids research, 2013 - academic.oup.com
Mitochondria and plastids (chloroplasts) are cell organelles of endosymbiotic origin that
possess their own genetic information. Most organellar DNAs map as circular double …
possess their own genetic information. Most organellar DNAs map as circular double …
[HTML][HTML] The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection
The Brassica genus encompasses three diploid and three allopolyploid genomes, but a
clear understanding of the evolution of agriculturally important traits via polyploidy is lacking …
clear understanding of the evolution of agriculturally important traits via polyploidy is lacking …