Jit
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GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
By Jit 3195 days agogithub.com - GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures Mapping position agnostic to alignment parameters. ...ACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 3013 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...WhatsHap: fast and accurate read-based phasing
By Jit 2840 days agowhatshap.readthedocs.io - WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. Features Very accurate...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2222 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 571 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood...
By Jit 3035 days agowww.sciencedirect.com - Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene...JASMINE: Jointly Accurate Sv Merging with Intersample Network Edges
By Shruti Paniwala 1344 days agogithub.com - This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine...GPOPSIM: a simulation tool for whole-genome genetic data
By Jit 2971 days agogithub.com - GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...SeqMonk:A tool to visualise and analyse high throughput mapped sequence data
By Jit 2734 days agowww.bioinformatics.babraham.ac.uk - SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic...ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 2241 days agogithub.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...
