Tags: EuGI, novel, genomic, islands, facilitate, horizontal, gene, transfer, detection, eukaryotes, tools
2184 days ago
Tags: Manta, rapid, detection, structural, variants, indels, germline, cancer, sequencing, applications
2168 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
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 red-black multipositional de Bruijn graph to detect...Tags: ReMILO, reference, assisted, misassembly, detection, algorithm, short, long, reads
2129 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
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. Contigs are assembled for every 25kb window (wi...Tags: SvABA, Genome-wide, detection, structural, variants, indels, local, assembly
1930 days ago
SeqMule: Automated human exome/genome variants detection
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 configuration file.Tags: SeqMule, Automated, human, exome, genome, variants, detection
1537 days ago
SvABA: Structural variation and indel detection by local assembly
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. Contigs are assembled for every 25kb window (wi...Tags: SvABA, Structural, variation, indel, detection, local, assembly
1516 days ago
ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes
ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in prokaryotes. https://www.mdpi.com/2073-4425/11/7/756/htm https://shadowcaster.r...Tags: ShadowCaster, hybrid, approach, detection, horizontal, gene, transfer, prokaryotes, HGT
1390 days ago
Platypus – R package for object detection and image segmentation.
platypus is an R package for object detection and semantic segmentation. Currently using platypus you can perform: multi-class semantic segmentation using U-Net architecture multi-class object detection using YOLOv3 architecture You can install the late...Tags: Platypus, R, package, object, detection, image, segmentation
1272 days ago