Aaryan Lokwani
A Bioinformatician
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MetaSim A Sequencing Simulator for Genomics and Metagenomics.
By Jit 3248 days agoab.inf.uni-tuebingen.de - Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a...jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 2649 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...HALC: High throughput algorithm for long read error correction
By Jit 3062 days ago Comments (1)github.com - HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2989 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 2352 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2890 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...PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 3000 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3255 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 3093 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 3086 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...
