dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testing1918 days ago
1867 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...caffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related referenc...1863 days ago
FLAS: fast and high throughput algorithm for PacBio long read self-correction.
FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.1797 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...caffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related referenc...1670 days ago
StringTie Transcript assembly and quantification for RNA-Seq
...st and highly efficient assembler of RNA-Seq alignments into potential transcripts. I...h gene locus. Its input can include not only alignments of short reads that can also...sed by other transcript assemblers, but also alignments of longer sequences that have...1444 days ago
1577 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://...1577 days ago
1571 days ago
pbmm2:A minimap2 frontend for PacBio native data formats
...s purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used di...1556 days ago