Rahul Nayak
A Bioinformatician
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Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 67 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 2541 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...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1434 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...FRODOCK 2.0: fast protein–protein docking server
By Neel 2228 days ago Comments (1)frodock.chaconlab.org - frodock: a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select...Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 1845 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler
By LEGE 1598 days agogithub.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...chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large...
By Jit 1023 days agogithub.com - chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons. USAGE: -query: sequence A in fasta format -db: sequence B in fasta format -out: output matrix -kmer Integer: k>1...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1420 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 2544 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...
