Abhimanyu Singh
A bioinformatics beginner
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R Graphs !!
By Jit 2970 days ago Comments (1)rgraphgallery.blogspot.be - The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided....Krona
By Jit 2832 days agogithub.com - Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2271 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2152 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...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1769 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...
Libraries or management tools for high throughput sequencing data
Last updated 79 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...BASE: a practical de novo assembler for large genomes using long NGS reads
By Rahul Nayak 2256 days agogithub.com - new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE...TGNet
By Shruti Paniwala 3042 days agogithub.com - Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2596 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...MinION_GC: An R script to do some QC on MinION data
By Radha Agarkar 2576 days agogithub.com - Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...
