Rahul Nayak
A Bioinformatician
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Common steps for reads mapping !
By BioStar 625 days agoMapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2265 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2062 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Understanding your reads and mapping !
By Neel 1760 days agobioinformatics-core-shared-training.github.io - One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.htmlSnakemake Tutorials !
By Rahul Nayak 929 days agocarpentries-incubator.github.io - A lesson introducing the Snakemake workflow system for bioinformatics analysis. Prerequisites This is an intermediate lesson and assumes learners have already done some bioinformatics: Familiarity with the BASH command shell, including...Public Databases for Bioinformatics !
By Jit 1341 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 2551 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 2542 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 2538 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...GIGGLE: a search engine for large-scale integrated genome analysis
By Jit 2509 days agogithub.com - GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is...
