Neel
Bioinformatics Beginner
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CLARK: Fast, accurate and versatile sequence classification system
By Jit 1722 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...ITIS: the Integrated Taxonomic Information System!
By Jit 1890 days agohttps://www.itis.gov/ - ITIS, the Integrated Taxonomic Information System! Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. We are a partnership of U.S., Canadian,...Unicycler: Hybrid assembly pipeline for bacterial genomes
By Jit 2548 days agogithub.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 2362 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...transrate: Understanding your transcriptome assembly
By Neel 2303 days agohibberdlab.com - Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This...ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
By BioStar 2143 days agogithub.com - The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...SvABA: Genome-wide detection of structural variants and indels by local assembly
By Abhimanyu Singh 2111 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1762 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...MEC: Contig Misassembly Correction
By BioStar 1732 days agogithub.com - MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on...SvABA: Structural variation and indel detection by local assembly
By Jit 1697 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....
