Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of...1705 days ago
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BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
With BioJupies you can produce in seconds a customized, reusable,...tive report from your own raw or processed RNA-seq data through a simple user interfa...for access to unlimited private notebooks, RNA-seq datasets and alignment jobs.1292 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and very fast....o clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FAST...1676 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to...be phylogenetic trees (or networks) and associated data. PhyloXML provides elements f...interoperability between various applications and databases. Furthermore, both due t...1671 days ago
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary informati...king procedure as well as test data are publicly accessible at th...umentation site http://biodatageeks.org/sequila/benchmarking...ject home page: http://biodatageeks.org/sequila/ • Sou...1664 days ago
Machine learning training and courses in bioinformatics !
Machine learning techniques have been successful in analyzing biological data because of their capabilities in handling randomness and uncertainty of data noise and in generalization....1647 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighte...gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whol...1644 days ago
RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the...1644 days ago