Rahul Agarwal
I'm a Bioinformatician and Programmer
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EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2180 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 1997 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...ngs-bits - Short-read sequencing tools
By Neel 1802 days agogithub.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources: Binaries for Linux/macOS From sources for Linux/macOS From sources for WindowsiSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1772 days agogithub.com - iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering,...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 1410 days agogithub.com - Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz...Public Databases for Bioinformatics !
By Jit 1371 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 2581 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 2572 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 2568 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 2539 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...
