BioStar
Bioinformatician
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nQuire: a statistical framework for ploidy estimation using next generation sequencing
By Jit 2864 days agogithub.com - nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2810 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...ngs-bits - Short-read sequencing tools
By Neel 2394 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 2364 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,...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1624 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Assistant Professor at Sher-e- Kashmir University of Agricultural Sciences & Technology of...
Sher-e- Kashmir University of Agricultural Sciences & Technology of Jammu School of Biotechnology Applications are invited from candidates for the temporary positions on contractual basis for academic arrangement in the School of...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2997 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...Troyanskaya Lab
The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods...Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2228 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By LEGE 341 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.
