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EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2710 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...Prof. Dr. med. Andreas Ramming
In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 2199 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...Artificial intelligence is more accurate than doctors in diagnosing breast cancer
By BioStar 2347 days agoArtificial intelligence is more accurate than doctors in diagnosing breast cancer from mammograms, a study in the journal Nature suggests.dna2bit: an ultra-fast and accurate genomic distance estimation software
By LEGE 279 days agogithub.com - dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2801 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...Cleaner BLAST Databases for More Accurate Results
By LEGE 774 days agoRemoving contaminated sequences using NCBI quality assurance toolsLAMSA: fast split read alignment with long approximate matches
By Jit 2944 days ago Comments (1)github.com - LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the...FLAS: fast and high throughput algorithm for PacBio long read self-correction.
By Jit 2540 days agogithub.com - FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes...SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
By Jit 2365 days agoacademic.oup.com - The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation...
