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@BilkentCompGen Alkan Lab for Bioinformatics and Computational Genomics

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    21 repositories

    • BilkentCompGen.github.io

      Public
      Alkan Lab website
      SCSS
      •7•3•0•0•Updated Dec 16, 2024Dec 16, 2024

    • gencore

      Public
      GenCore utilizes the innovative Locally Consistent Parsing (LCP) algorithm for precise genomic comparisons, supporting .fastq, .bam, and .fasta files. Implemented in C++ for high performance on large datasets
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

    • lcptools

      Public
      The string class contains algorithm that runs lcp on given string and alphabet encoding
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

    • GateKeeper-GPU

      Public
      Pre-Alignment Filtering for Short Read Mapping in GPU
      C
      •1•3•0•0•Updated Jun 27, 2024Jun 27, 2024

    • saber

      Public
      Pattern matching tool to detect block rearrangement events in genomic sequences
      C++
      •0•1•0•0•Updated Feb 14, 2024Feb 14, 2024

    • Linden

      Public
      C++
      •1•0•0•0•Updated Oct 15, 2023Oct 15, 2023

    • tardis

      Public
      Toolkit for automated and rapid discovery of structural variants
      C
      •
      BSD 2-Clause "Simplified" License
      •6•21•3•0•Updated Aug 24, 2023Aug 24, 2023

    • brifin

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jan 2, 2023Jan 2, 2023

    • valor

      Public
      variation discovery using long range information in linked-reads
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •2•15•5•0•Updated Oct 5, 2021Oct 5, 2021

    • mrcanavar

      Public
      micro-read Copy Number Variant Regions finder
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •2•10•0•0•Updated Feb 24, 2021Feb 24, 2021

    • bibliography

      Public
      0•0•0•0•Updated Nov 3, 2020Nov 3, 2020

    • mam

      Public
      Multiple alignment Manipulator
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 15, 2020Apr 15, 2020

    • mrfast

      Public
      micro-read Fast Alignment Search Tool
      C
      •
      Other
      •4•19•1•1•Updated Jul 19, 2019Jul 19, 2019

    • sonic-prebuilt

      Public
      Prebuilt SONIC files for different genomes.
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 18, 2019Jul 18, 2019

    • GateKeeper

      Public
      GateKeeper: Fast Alignment Filter for DNA Short Read Mapping
      VHDL
      •
      GNU General Public License v3.0
      •9•18•0•0•Updated Mar 5, 2019Mar 5, 2019

    • lava

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Aug 16, 2018Aug 16, 2018

    • hercules

      Public
      Profile HMM-based hybrid error correction algorithm for long reads
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•20•6•0•Updated Aug 15, 2018Aug 15, 2018

    • repeatnet

      Public
      RepeatNet: an ab initio centromeric sequence detection algorithm
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Aug 4, 2017Aug 4, 2017

    • sirfast

      Public
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 4, 2017Aug 4, 2017

    • drfast

      Public
      dibase-read Fast Alignment Search Tool
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 4, 2017Aug 4, 2017

    • MAGNET

      Public
      MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering
      MATLAB
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•0•0•Updated Aug 4, 2017Aug 4, 2017