Manisha Mishra
A Bioinformatician
Our Sponsors
Related items
UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and...
By BioStar 579 days agoikim-essen.github.io - UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment Using state of the art tools, easily extended for other viruses Tool and database updates for critical components via...Genome Simulation with SLiM and msprime
By BioStar 400 days agoSLiM and msprime are valuable tools for genome simulation, each serving distinct but complementary purposes in population genetics research. By leveraging the strengths of both simulators with slendr, researchers can conduct robust and efficient...CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
By Shruti Paniwala 1382 days agogitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...bpRNA: large-scale automated annotation and analysis of RNA secondary structure
By Rahul Nayak 2846 days agogithub.com - bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2802 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...FLAS: fast and high throughput algorithm for PacBio long read self-correction.
By Jit 2451 days agogithub.com - FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3578 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 3040 days agogithub.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...SWALO: Scaffolding with assembly likelihood optimization
By Jit 2818 days agoatifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via...
By Jit 2671 days agogithub.com - MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to...
