Studies structural variant callers on large simulated populations sequenced with PacBio CCS
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Updated
Mar 12, 2023 - C++
Studies structural variant callers on large simulated populations sequenced with PacBio CCS
A metagenome assembly and evaluation pipeline, focused on hi-fi long reads, but with support for lo-fi long reads and hybrid assemblies
Evolutionary genomics of chromosomal inversions in Atlantic herring
Target site duplication assessment from alignment file and genomic location of insertion sites.
GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. at https://people.inf.ethz.ch/omutlu/pub/GenS…
Benchmarking for long-reads assembler
Annotate MEI in a VCF file containing sequence-resolved structural variation calls
Assembly of chloroplast genome using long-reads and short-reads for Genomics Course 2021 (MSc Bioinformatics for Computational Genomics)
Reference-free Binning of Metagenomics Long Reads using Coverage and Composition
SV genotyper for long reads with a variation graph
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
ORI (Oxford nanopore Reads Identification) is a software allowing, from long nanopore reads, to identify the bacterial strains present in a sample.
Elloreas, a genome assembler
KNOT: Knowledge Network Overlap exTraction is a tool for the investigation of fragmented long read assemblies.
Scripts for the Nature Biotechnology paper, 2020: Automated assembly of centromeres from ultra-long error-prone reads
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
Long Reads Mapping Algorithms
nPoRe: n-Polymer Realigner for improved pileup-based variant calling
A short tandem repeat (STR) genotyping and analysis toolkit for long reads
YAGCloser: Yet-Another-Gap-Closer based on spanning of long reads.
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