BC Cancer Canada's Michael Smith Genome Sciences Centre

Repositories

• tigmint

  ⛓ Correct misassemblies using linked AND long reads

  bioinformatics genome-assembly genome-scaffolding 10xgenomics misassembly-correction linked-reads bioinformatics-tool
  Python GPL-3.0 7 32 1 0 Updated Aug 25, 2020

• pori_graphkb_python

  Python adapter package for querying the GraphKB API

  bioinformatics annotation
  Python GPL-3.0 0 1 0 1 Updated Aug 24, 2020

• pori_ipr_python

  Python adapter for generating reports uploaded to IPR using the PORI platform

  bioinformatics genomics reporting
  Python GPL-3.0 0 1 0 1 Updated Aug 24, 2020

• xmatchview

  🗻 Visualization of genome/gene sequence synteny
  Python GPL-3.0 2 15 0 0 Updated Aug 24, 2020

• LINKS

  ⛓Long Interval Nucleotide K-mer Scaffolder

  bloom-filter scaffold long-reads draft-assembly extract-kmer-pairs genome-assemblies scaffold-layout
  Perl GPL-3.0 12 44 1 4 Updated Aug 24, 2020

• RAILS

  🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling
  Perl GPL-3.0 6 18 2 1 Updated Aug 24, 2020

• HLAminer

  ⛏HLA predictions from NGS shotgun data

  alignments oxford-nanopore hla-prediction targeted-assemblies hla-sequence shotgun-sequence-datasets
  Perl 10 24 0 0 Updated Aug 24, 2020

• SSAKE

  🍶Genome assembly with short sequence reads

  dna-sequences genome-scaffolding short-reads sequence-assembly genome-assembler read-pairs
  Perl GPL-2.0 4 13 0 0 Updated Aug 24, 2020

• ntEdit

  ✏️ultra fast and scalable genome assembly polishing

  c-plus-plus bloom-filter polishing draft-genome variant-detection
  C++ GPL-3.0 4 42 0 0 Updated Aug 24, 2020

• physlr

  ⛓️ Construct a Physical Map from Linked Reads

  bioinformatics genome-assembly genome-scaffolding 10xgenomics linked-reads bioinformatics-tool
  Python GPL-3.0 5 10 10 5 Updated Aug 24, 2020

• mavis

  Merging, Annotation, Validation, and Illustration of Structural variants

  visualization python bioinformatics genomics transcriptome structural-variation
  Python 7 37 11 1 Updated Aug 22, 2020

• RNA-Bloom

  🌺 lightweight transcriptome assembly for short reads and nanopore reads

  rna-seq denovo-assembly single-cell-rna-seq bioinformatics-tool nanopore-sequencing
  Java 1 29 2 0 Updated Aug 19, 2020

• straglr
  Python 0 2 0 0 Updated Aug 18, 2020

• btl

  🔬 Bioinformatics Technology Lab, Genome Sciences Centre
  HTML 2 0 4 0 Updated Aug 17, 2020

• RNA-Scoop

  interactive visualization of single-cell transcriptomes

  data-visualization single-cell-rna-seq
  Java 0 4 0 0 Updated Aug 14, 2020

• ntHash

  ntHash: recursive nucleotide hashing

  bioinformatics genomics bloom-filter hash hash-algorithm hash-methods k-mer-hashing
  C++ MIT 6 46 2 1 Updated Aug 14, 2020

• GapPredict

  Character-level language model for draft genome assembly gap-filling
  Python GPL-3.0 0 0 0 1 Updated Aug 13, 2020

• abyss

  🔬 Assemble large genomes using short reads

  science c-plus-plus bioinformatics genome bloom-filter assembler scaffold
  C++ 87 204 4 1 Updated Aug 12, 2020

• NanoSim

  Nanopore sequence read simulator

  simulator genome transcriptome oxford-nanopore nanopore-sequencing
  Python 27 76 10 1 Updated Aug 9, 2020

• biobloom

  Create Bloom filters for a given reference and then use it to categorize sequences
  C++ 10 58 11 0 Updated Jul 31, 2020

• btl_bloomfilter

  The BTL C/C++ Common bloom filters for bioinformatics projects, as well as any APIs created for other programming languages.
  C++ GPL-3.0 2 11 1 1 Updated Jul 31, 2020

• pavfinder

  🔍 Post Assembly Variants Finder
  Python 1 8 0 0 Updated Jul 25, 2020

• ntJoin

  🔗Genome assembly scaffolder using minimizer graphs
  Python GPL-3.0 8 34 1 0 Updated Jul 13, 2020

• arcs

  🌈Scaffold genome sequence assemblies using linked read sequencing data

  science c-plus-plus bioinformatics genome graph assembler scaffold
  C++ GPL-3.0 12 54 2 3 Updated Jul 13, 2020

• qupath-annotation-exchange

  An extension for QuPath for importing JSON annotations made in a GSC internal application
  Java 0 1 0 0 Updated Jun 12, 2020

• kollector

  de novo targeted gene assembly
  Shell 4 20 5 2 Updated May 11, 2020

• ntCard

  Estimating k-mer coverage histogram of genomics data

  hyperloglog cardinality-estimation k-mer-counting k-mer-frequency streaming-algorithms
  C++ MIT 4 59 0 0 Updated May 8, 2020

• AMPlify

  Attentive deep learning model for antimicrobial peptide prediction
  Python GPL-3.0 0 1 0 0 Updated Apr 8, 2020

• Terminitor

  Deep Neural Network model that predicts polyadenylation sites

  deep-neural-networks deeplearning polyadenylation
  Python GPL-3.0 1 4 1 0 Updated Feb 13, 2020

• ntHits

  Identifying repeats in high-throughput sequencing data
  C++ MIT 0 5 3 1 Updated Jan 30, 2020