BOL

github.com - FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise...

www.seqan.de - STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X...

github.com - FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes...

github.com - 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 bulk RNA-seq (strand-specific/agnostic) paired-end single-cell RNA-seq...

github.com - fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect...

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 - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...

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 - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...

github.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly...