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UCSC SARS-CoV-2 Genome Browser
By Jit 1030 days agowww.nature.com - The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar...Environmental Genomics Group SciLifeLab/KTH Stockholm
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By LEGE 213 days agoCost-effective whole human genome sequencing has revolutionized the landscape of genetic research and personalized medicine by making comprehensive genetic analysis accessible to a wider population. Through advancements in sequencing technologies,...SISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2165 days agogithub.com - Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2353 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...COSINE: non-seeding method for mapping long noisy sequences
By Jit 2198 days agogithub.com - Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long...UPhO: Scripts for homology and orthology assessment from genomic sequences.
By BioStar 2118 days agogithub.com - UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help. The only input requierement for UPhO...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 1696 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...Tiara: deep learning-based classification system for eukaryotic sequences
By Rahul Nayak 962 days agoacademic.oup.com - With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of...
