2191 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predict...2184 days ago
2183 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but wor...2178 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
..../minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax sr ref....2155 days ago
Epiviz: an interactive visualization tool for functional genomics data.
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like...her genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, h...2136 days ago
SimLoRD: A read simulator for third generation sequencing reads
...ents may be incorporated at a later stage.) The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existi...2091 days ago
STELLAR: fast and exact local alignments
STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar.2084 days ago
SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
...It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features...2072 days ago
S-plot2: creates an interactive, two-dimensional heatmap of sequences
S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2,...2055 days ago