Jit
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SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1433 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 2484 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...WhatsHap: fast and accurate read-based phasing
By Jit 2370 days agowhatshap.readthedocs.io - WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Features Very accurate...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2277 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...ANItools web: a web tool for fast genome comparison within multiple bacterial strains
By Jit 2200 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 1836 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...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1427 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 258 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,...Molecular Genetics Lecture
By Rahul Agarwal 4074 days agowww.youtube.com - "Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and...Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
By Poonam Mahapatra 2365 days agomolevol.cmima.csic.es - Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...
