TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Trit...1729 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
...ignificantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly parallel and accurate pre-ali...1653 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo&n...1435 days ago
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BlobToolKit: A toolkit for genome assembly QC
...nts: BlobToolKit Viewer allows browser-based interactive visualisation and filtering of preliminary or published genomic datasets even for highly fragmented assemblies. BlobT...1544 days ago
flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of c...1481 days ago
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
...on Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as g...1457 days ago
SEASTAR: Systematic Evaluation of Alternative STArt site in RNA
...NA-Seq data and merges them with known TSSs from a public database. This package enables high-quality TSS identification that is comparable to the highly sophisticated CAGE technology...1370 days ago
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