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PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the...
By BioStar 2822 days agogithub.com - Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via: sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config On MacOS, the Apple...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 2351 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 3109 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...CLARK: Fast, accurate and versatile sequence classification system
By Jit 2311 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Abhi 1711 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 827 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 264 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...SeqCAT: Sequence Conversion and Analysis Toolbox
By Neel 729 days agomtb.bioinf.med.uni-goettingen.de - Your all-in-one solution for smooth conversion of sequence coordinates. Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate...CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
By Jit 3245 days agowebchem.ncbr.muni.cz - Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized...Scripts for the analysis of HGT in genome sequence data.
By Jit 3118 days agogithub.com - Scripts for the analysis of HGT in genome sequence data
