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By LEGE 224 days agogithub.com - Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 2371 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...Artificial intelligence is more accurate than doctors in diagnosing breast cancer
By BioStar 1774 days agoArtificial intelligence is more accurate than doctors in diagnosing breast cancer from mammograms, a study in the journal Nature suggests.HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from...
By BioStar 1688 days agogithub.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More...Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 1417 days agogithub.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2228 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 201 days agoRemoving contaminated sequences using NCBI quality assurance toolsClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
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By Jit 2528 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2319 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...
