Abhimanyu Singh
A bioinformatics beginner
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nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2122 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 1739 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 49 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...Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
By Shruti Paniwala 2220 days agowww.well.ox.ac.uk - Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 1760 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...RCircos: an R package for Circos 2D track plots
By Jit 3108 days agobitbucket.org - RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It...Sushi: An R/Bioconductor package for visualizing genomic data
By Jit 3005 days agowww.bioconductor.org - Sushi: An R/Bioconductor package for visualizing genomic dataR-chie
By Jit 3004 days agowww.e-rna.org - R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2566 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 2546 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...
