BOL

github.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...

github.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures    Mapping position agnostic to alignment parameters.   ...

github.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...

github.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...

japsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...

github.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....

gite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...

github.com - Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful...

github.com - 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 identity (higher is better) when choosing which reads pass the...

github.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...