Pinned Repositories
hercules
Profile HMM-based hybrid error correction algorithm for long reads
reproducibility
sanity check scripts
BilkentCompGen.github.io
CrossMap
CrossMap is a python program to lift over genome coordinates from one genome version to another.
EmotionEngine
twtagger
Tweet hashtag recommendation
AirLift
AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at http://arxiv.org/abs/1912.08735)
Apollo
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-technology-independent-genome-assembly-polishing_bioinformatics20.pdf
BLEND
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
RawHash
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).
canfirtina's Repositories
canfirtina/CrossMap
CrossMap is a python program to lift over genome coordinates from one genome version to another.
canfirtina/EmotionEngine
canfirtina/twtagger
Tweet hashtag recommendation
canfirtina/BilkentCompGen.github.io
canfirtina/bioconda-recipes
Conda recipes for the bioconda channel.
canfirtina/canfirtina.github.io
al-folio template for canfirtina.github.io
canfirtina/CHM13-issues
CHM13 human reference genome issue tracking
canfirtina/EtrafaSor
EtrafaSor
canfirtina/FirstOpenCLProgram
canfirtina/hercules-1
Profile HMM-based hybrid error correction algorithm for long reads
canfirtina/HybridErrorCorrection
canfirtina/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
canfirtina/OpenCLWithBestGPU
Detects all the GPUs in devices, and choses (relatively) best one to maintain the further computation.
canfirtina/QtOpenCLGLInterop
Iteroperability test of OpenGL and OpenCL using Qt
canfirtina/sigmap
A streaming method for mapping nanopore raw signals
canfirtina/UNCALLED
Raw nanopore signal mapper that enables real-time targeted sequencing
canfirtina/VectorAdditionOpenCL