LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
...of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering. https://github.com/CSB5/lof...1535 days ago
BlobToolKit: A toolkit for genome assembly QC
Filtering raw genomic datasets is essential to avoid chimer...approach to simplify interactive and reproducible filtering. BlobToolKit is comprised of...llows browser-based interactive visualisation and filtering of preliminary or published g...1532 days ago
1496 days ago
Filtlong: quality filtering tool for long reads
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read id...1450 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 mag...1229 days ago
FiNGS: Filters for Next Generation Sequencing
...s Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to u...s. It allows users to develop and implement their own filtering strategies and simple sharing...1160 days ago
843 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer...759 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
...users can choose a supermatrix approach and/or gene tree inference followed by supertree reconstruction. Users can specify a range of alignment filtering settings to retain high-quali...71 days ago
ExRec: Exclusion of Recombined DNA
...ications: the first two convert folders of NEXUS or PHYLIP files into the standard input file for the main program that conducts the four-gamete filtering procedures. The pipeline outp...35 days ago