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VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2242 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...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2392 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1640 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...ngs-bits - Short-read sequencing tools
By Neel 1773 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 WindowsBFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing...
By Jit 2368 days agogithub.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...NanoPack: visualizing and processing long-read sequencing data
By Jit 2160 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2487 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2410 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...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2150 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 2123 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...
