Official GitHub repository:

• https://github.com/BilkentCompGen

Docker Hub repository

• https://hub.docker.com/u/alkanlab/

High Throughput sequencing

• mrFAST: Read mapper developed specifically for structural variation and segmental duplication detection using the Illumina platform. Supports small indel alignments.
• mrsFAST: Similar to mrFAST, Hamming distance only.
• mrCaNaVaR: Read depth analysis method to characterize segmental duplications and predict absolute copy numbers.
  
• SCALCE: Tool to efficiently compress FASTQ files.
• TARDIS: Toolkit for automatic and rapid discovery of structural variants.
• Pamir: Discovery and genotyping of novel sequence insertions in many sequenced individuals.
• VALOR2: Discover inversions using long range information -- linked-read version.
• GateKeeper: FPGA design for accelerating pre-alignment in DNA short read mapping.
• GateKeeper-GPU: GPGPU design for accelerating pre-alignment in DNA short read mapping.
• MAGNET: FPGA-based filtering strategy with high accuracy across different edit distance thresholds.
• Shouji: Fast and efficient computation of banded sequence alignment.
• SneakySnake: Approximate alignment computation on CPU, GPU, and FPGA by reducing alignment problem to single net routing problem.
• Hercules: Profile HMM-based hybrid error correction algorithm for long reads.
• Apollo: Profile HMM-based genome assembly polishing tool.
• RinsLR: Discovery of mid range novel sequence insertions using long-read sequencing.
• DeCoNT: CNV prediction polisher on whole exome sequencing data.
• GenASM: approximate string matching (ASM) acceleration framework for genome sequence analysis.
• SeGraM: universal genomic mapping accelerator that supports both sequence-to-graph mapping and sequence-to sequence mapping, for both short and long reads.
• FastRemap: Tool for quickly remapping reads between genome assemblies.
• BLEND: Fast, memory-efficient, and accurate mechanism to find fuzzy seed matches in genome analysis.
• AirLift: Fast and comprehensive technique for translating alignments between reference genomes.
• TargetCall: Pre-basecalling filter for nanopore sequencing.
• LCPan: Variation graph construction using Locally Consistent Parsing.

Others

• MaM: A software tool that processes and manipulates multiple alignments of genomic sequences.
• BISER: Characterization of segmental duplication evolutionary structure across genome assemblies.
• BriFin: Tool designed to detect specialized hubs among the proteins providing cell-to-cell interactions in protein-protein interaction networks that include the proteins of two interacting cells.
• SABER: Tool to perform pairwise sequence alignment using block edits and rearrangements.
• Linden: Alternating Lyndon Factorization Tree data structure and its application to whole-genome alignments.
• LCPtools: Implementation of the Locally Consistent Parsing (LCP) algorithm for string processing as an API.
• GenCore: Fast alignment-free genomic distance estimation using LCP.

Deprecated Tools

• High Throughput Sequencing
  

  • drFAST: Read mapper for di-base color-space reads generated with the SOLiD platform.
  • sirFAST: Read mapper for short interrupted reads generated with the Complete Genomics platform.
  • VariationHunter: Structural variation calling algorithm using read pair mapping information including suboptimal alignments. (replaced by TARDIS)
  • SPLITREAD: Detection of structural variants and indels from genome and exome sequencing data.
  • NovelSeq: Novel sequence insertion discovery framework. (replaced by Pamir)
  • VALOR: Discover inversions using long range information.(replaced by VALOR2)

• RNA analysis
  

  • taveRNA suite
  • inteRNA: Algorithm that predicts the joint secondary structure of two RNA sequences.
    
  • alteRNA: Densityfold algorithm that minimizes a linear combination of energy density and the total free energy.
  • pRuNA: RNA interaction search engine. pRuNA is a sequence based pruning technique that eliminates a significant fraction of a non coding RNA (ncRNA) data set and retains only the most likely ncRNA candidates for forming a stable joint structure with the query mRNA.
    
  • piRNA: RNA-RNA interaction partition function algorithm to predict the joint partition function, equilibrium concentration, ensemble energy, and melting temperature for two RNA sequences.
    
  • smyRNA: Novel ab initio non-coding RNA finder.
    

  • Others
    

    • RepeatNet: An ab initio centromeric sequence detection algorithm.
    • SEDEF: Characterization of segmental duplications within genome assemblies. (replaced by BISER)