Jit
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Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
By Jit 2106 days agosupport.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...Mercator: Multiple Whole-Genome Orthology Map Construction
By Jit 2117 days agowww.biostat.wisc.edu - Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an...KAST: Perform Alignment-free k-tuple frequency comparisons from sequences
By Jit 2725 days agogithub.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 3010 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...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2436 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1903 days agogithub.com - 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 magnitude) expedites sequence alignment calculation for both short...MUMmer4: A fast and versatile genome alignment system
By Jit 2954 days agomummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2844 days agogithub.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,...ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2670 days agohttp://ani.mypathogen.cn/ - ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you...mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 2305 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...
