BC Cancer Canada's Michael Smith Genome Sciences Centre

NanoSim

Nanopore sequence read simulator

simulator genome transcriptome oxford-nanopore nanopore-sequencing

Python 27 74 10 0 Updated Aug 9, 2020

abyss

🔬 Assemble large genomes using short reads

science c-plus-plus bioinformatics genome bloom-filter assembler scaffold

C++ 86 204 4 1 Updated Aug 9, 2020

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 6 4 Updated Aug 7, 2020

RNA-Scoop

interactive visualization of single-cell transcriptomes

data-visualization single-cell-rna-seq

Java 0 4 0 0 Updated Aug 7, 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 2 Updated Aug 7, 2020

straglr

Python 0 2 0 0 Updated Aug 7, 2020

pori_graphkb_python

Python adapter package for querying the GraphKB API

bioinformatics annotation

Python GPL-3.0 0 1 0 0 Updated Aug 7, 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 5, 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 5, 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 5, 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 5, 2020

xmatchview

🗻 Visualization of genome/gene sequence synteny

Python GPL-3.0 2 15 0 0 Updated Aug 5, 2020

RAILS

🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling

Perl GPL-3.0 6 18 2 1 Updated Aug 5, 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 4 Updated Aug 1, 2020

biobloom

Create Bloom filters for a given reference and then use it to categorize sequences

C++ 10 57 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 24, 2020

mavis

Merging, Annotation, Validation, and Illustration of Structural variants

visualization python bioinformatics genomics transcriptome structural-variation

Python 7 36 11 1 Updated Jul 17, 2020

btl

🔬 Bioinformatics Technology Lab, Genome Sciences Centre

HTML 2 0 4 0 Updated Jul 16, 2020

ntJoin

🔗Genome assembly scaffolder using minimizer graphs

Python GPL-3.0 7 32 2 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 11 54 2 3 Updated Jul 13, 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 Jun 18, 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

ntHash

ntHash: recursive nucleotide hashing

bioinformatics genomics bloom-filter hash hash-algorithm hash-methods k-mer-hashing

C++ MIT 6 45 2 2 Updated Jun 11, 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 58 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

transabyss

de novo assembly of RNA-seq data using ABySS

bioinformatics rna-seq transcriptome transcriptome-assembly

Python 6 17 1 0 Updated Jan 20, 2020