Jit
Enthusiast computational biologist with business dream !!!
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karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2958 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2882 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2622 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...nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2595 days agogithub.com - nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 1853 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...FiNGS: Filters for Next Generation Sequencing
By Neel 1837 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...ngs-bits - Short-read sequencing tools
By Neel 2244 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 WindowsThe Genome 10K Project
By Jit 4242 days agohttps://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction...Indexcov: fast coverage quality control for whole-genome sequencing
By Jit 2750 days ago Comments (1)github.com - indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2863 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...
