Abhimanyu Singh
A bioinformatics beginner
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Strudel
By Anjana 3445 days agoics.hutton.ac.uk - Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual...gbtools: Interactive Visualization of Metagenome Bins in R
By Jit 3268 days agojournal.frontiersin.org - We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of...DESCHRAMBLER
By Jit 3173 days agogithub.com - DESCHRAMBLER is shown to produce highly accurate reconstructions using data simulation and by benchmarking it against other reconstruction tools You can find the detail of reconstructed data at http://bioinfo.konkuk.ac.kr/DESCHRAMBLER/fragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2854 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...Synteny and Rearrangement Identifier (SyRI)
By Jit 2132 days agoschneebergerlab.github.io - SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI...Synteny Portal: a web-based application portal for synteny block analysis
By Jit 3209 days agobioinfo.konkuk.ac.kr - Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 168 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...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2853 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...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2669 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 2380 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAP
