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 n...1430 days ago
modelStudio: a package automates the explanation of machine learning predictive models
...r model exploration unite with tools for EDA (Exploratory Data Analysis) to give a broad overview of the model behavior. modelStudio is a fast and condensed way to get all...1568 days ago
CLARK: Fast, accurate and versatile sequence classification system
CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the arti...1545 days ago
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities an...1542 days ago
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.1469 days ago
RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types: single-end/paired-end b...1400 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
...of plots (barplot, boxplot, heatmap, …).The bioinformatics treatment is based on Vsearch [Rognes 2016] which showed to be both accurate and fast [Wescott 2015].The statistica...1361 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calli...1287 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact ...1275 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of m...1236 days ago