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gSearch: a fast and flexible general search tool for whole-genome sequencing
By Jit 2770 days agoml.ssu.ac.kr - gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2739 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2672 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLjackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 2417 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...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2231 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...BreakSeq2
By Jitendra Narayan 3659 days agobioinform.github.io - Ultrafast and accurate nucleotide-resolution analysis of structural variants More at http://bioinform.github.io/breakseq2/ Download BreakSeq2 Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gzFor other versions, see...GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 2192 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...CONTIGuator !
By BioStar 2347 days agosourceforge.net - CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
By Jit 3023 days agokiwi.cs.dal.ca - RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to...BioCircos.js is an open source interactive Javascript library to interactive display biological...
By Jit 2969 days agobioinfo.ibp.ac.cn - BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript...
