Shruti Paniwala
A Bioinformatician
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Resolving the complexity of the human genome using single-molecule sequencing
By Rahul Agarwal 4103 days agowww.nature.com - The human genome is arguably the most complete mammalian reference assembly yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. The results in this paper...SeqMule: Automated human exome/genome variants detection
By BioStar 2420 days agodoc-openbio.readthedocs.io - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 3229 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 3064 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...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2949 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...Artificial intelligence is more accurate than doctors in diagnosing breast cancer
By BioStar 2468 days agoArtificial intelligence is more accurate than doctors in diagnosing breast cancer from mammograms, a study in the journal Nature suggests.Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 2110 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...dna2bit: an ultra-fast and accurate genomic distance estimation software
By LEGE 399 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 2922 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,...
