Processing and Analyzing Multiple Genomes Alignments with MafFilter.
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-0199-0_2
Abstract: As the number of available genome sequences from both closely related species and individuals within species increased, theoretical and methodological convergences between the fields of phylogenomics and population genomics emerged. Population genomics typically focuses on… read more here.
Keywords: analyzing multiple; processing analyzing; multiple genomes; genome alignments ... See more keywords
chainCleaner improves genome alignment specificity and sensitivity
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btx024
Abstract: Motivation: Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements. Results: Here we present a fast approach, called chainCleaner,… read more here.
Keywords: chaincleaner improves; genome alignments; sensitivity; improves genome ... See more keywords
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
Sign Up to like & getrecommendations! Published in 2020 at "GigaScience"
DOI: 10.1093/gigascience/giaa047
Abstract: Abstract Background Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on… read more here.
Keywords: full genome; whole genome; genome alignments; synteny block ... See more keywords
Pangenome graph construction from genome alignments with Minigraph-Cactus
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DOI: 10.1101/2022.10.06.511217
Abstract: Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs,… read more here.
Keywords: reference; pangenome graph; genome alignments; minigraph cactus ... See more keywords