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Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 3207 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 3067 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...
Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4830 days ago320000 viruses in mammals yet to sequenced in future!!!
By Rahul Agarwal 4782 days ago70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3228 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...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 3058 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,...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 382 days agogithub.com - HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 2118 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...JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
By Jit 3022 days agogithub.com - JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2441 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...
