Jit
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kebabs: package provides functionality for kernel based analysis of biological sequences via...
By Rahul Nayak 997 days agowww.bioinf.jku.at - The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define...RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
By Jit 2554 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...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2411 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2243 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...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2151 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2124 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...Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical...
By Jit 1769 days agodeltarho.org - Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment. For those familiar with Trellis...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1741 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...Submit your SARS-CoV-2 sequence data to GenBank
By Neel 1690 days agoSubmit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page.McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1490 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....
