Explore @bcgsc Open Source projects

BC Cancer Canada's Michael Smith Genome Sciences Centre (@bcgsc)

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abyss

🔬 Assemble large genomes using short reads

NanoSim

Nanopore sequence read simulator

ntHash

Fast hash function for DNA/RNA sequences

RNA-Bloom

🌺 reference-free transcriptome assembly for short and long reads

arcs

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

ntJoin

🔗Genome assembly scaffolder using minimizer graphs

ntCard

Estimating k-mer coverage histogram of genomics data

biobloom

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

LINKS

⛓ Long Interval Nucleotide K-mer Scaffolder

mirna

microRNA profiling pipeline

mavis

Merging, Annotation, Validation, and Illustration of Structural variants

ntSynt

Detecting multi-genome synteny using minimizer graph mapping

straglr

Tandem repeat expansion detection or genotyping from long-read alignments

ntEdit

✏️ Genome assembly polishing & SNV detection

tigmint

⛓ Correct misassemblies using linked AND long reads

HLAminer

⛏ HLA predictions from NGS shotgun data

orca

🐳 Genomics Research Container Architecture

LongStitch

Correct and scaffold assemblies using long reads

AMPlify

Attentive deep learning model for antimicrobial peptide prediction

xmatchview

🗻 Visualization of genome/gene sequence synteny

goldrush

Linear-time de novo Long Read Assembler

transabyss

de novo assembly of RNA-seq data using ABySS

ntLink

Minimizer-based assembly scaffolding and mapping using long reads

pori

Platform for Oncogenomic Reporting and Interpretation (PORI)

RAILS

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

SSAKE

🍶 Genome assembly with short sequence reads

btllib

Bioinformatics Technology Lab common code library

kollector

de novo targeted gene assembly

btl_bloomfilter

The BTL C/C++ Common bloom filters for bioinformatics projects, as well as any APIs created for other programming languages.

physlr

⛓️ Construct a Physical Map from Linked Reads

pavfinder

🔍 Post Assembly Variants Finder

ntEmbd

Deep learning embedding for nucleotide sequences

chromeqc

ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads

ntHits

Identifying repeats in high-throughput sequencing data

ChopStitch

Finding putative exons and constructing splicegraphs using Trans-ABySS contigs

unikseq

🧬 Unique (& conserved) DNA sequence identification

mtGrasp

mtGrasp: de novo reference-grade mitochondrial genome assembly and standardization

RNA-Scoop

:shipit: interactive visualization of single-cell transcriptomes

abyss-2.0-giab

🍼 Assemble the Genome in a Bottle sequencing data

arks

ARCHIVED 🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads. ARCS/ARKS projects have been consolidated: https://github.com/bcgsc/arcs

pori_graphkb_client

Front-end web client for the GraphKB project

pori_ipr_api

Integrated Pipeline Reports (IPR) API, the reporting API as part of the PORI platform

pori_ipr_client

Integrated Pipeline Reports (IPR) client. The web interface for the reporting application as part of PORI

pori_graphkb_python

Python adapter package for querying the GraphKB API

tAMPer

tAMPer: antimicrobial peptides toxicity prediction

Jupyter Notebook

TASR

Targeted Assembly of Short Reads

PASS

Proteome Assembler with Short peptide Sequence

rAMPage

rAMPage: Rapid AMP Annotation and Gene Estimation

ABySS-explorer

Visualize genome sequence assemblies

pori_graphkb_loader

The Loaders for GraphKB. Imports content from external sources via the GraphKB REST API

pori_ipr_python

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

ntedit_sealer_protocol

Efficient targeted error resolution and automated finishing of long-read genome assemblies

Trans-NanoSim

Oxford nanopore transcriptome read simulator

Terminitor

Deep Neural Network model that predicts polyadenylation sites

GapPredict

Character-level language model for draft genome assembly gap-filling

goldpolish

GoldPolish (aka GoldRush-Edit) is a long read sequence polisher used in the GoldRush assembler

pori_graphkb_schema

Shared package between the API and GUI for GraphKB which holds the schema definitions and schema-related functions

tasrkleat-TCGA-analysis-scripts

This repo stores codes for the analysis of tasrkleat results on TCGA RNA-Seq dataa

Jupyter Notebook

rnaseq_utils

utility scripts for RNA-seq data

pori_graphkb_parser

A package for parsing and recreating HGVS-like variant notation used in GraphKB

pori_graphkb_api

REST API for the GraphKB project

peekseq

De novo protein-coding potential calculator using a k-mer approach

bloom-identity-est

These scripts provide a fast, memory-efficient method for estimating the percent sequence identity between two genomes using a probabilistic data structure called a Bloom filter

ntRoot

🌳 Human ancestry inference from genomic data

TMBur

Derive TMB estimates from whole genome fastq files. Runs alignment and variant calling before reporting a variety of TMB estimates

Canadian_Biogenome_Project

This repo contains the pipeline used by the Canadian Biogenome Project (http://earthbiogenome.ca) to generate assemblies

gum

GUM: Group, User Manager for LDAP

dida

sqlalchemy_hawq

Custom dialect for using SQLAlchemy with a HAWQ database which extends the postgres dialect

graphviz-utils

GraphViz scripts

Mito-AssemblyViz

Mitochondrial Genome Assembly Assessment Visualization

qupath-annotation-exchange

An extension for QuPath for importing JSON annotations made in a GSC internal application

pori_cbioportal

cBioportal adaptor for creating PORI reports in IPR

tr_catalog

Tandem repeat catalog from public long-read sequence assemblies

link_str

Analysis scripts developed for genotyping STRs in linked-read data

ggcli

command line interface for ggplot

abyss-organelle

Utilities to assemble an organelle genome using ABySS

long_read_pog

Analysis code for a cohort of Nanopore-sequenced tumours.

IMPALA

Integrated Mapping and Profiling of Allelically-expressed Loci with Annotations

lcm

abyss-connector-paper

ABySS-Connector: Connecting Paired Sequences with a Bloom Filter de Bruijn Graph

picea-glauca-plastid

🌲 Annotate the plastid genome of white spruce (Picea glauca)

rsempipeline

A pipeline for running rsem analysis on thousands of samples

Stash

This repository contains the implementation for the Stash data structure

picea-engelmannii-plastid

🌲 Annotate the plastid genome of Engelmann spruce (Picea engelmannii)

AMPd-Up

De novo antimicrobial peptide sequence generation with recurrent neural networks

btl

🔬 Bioinformatics Technology Lab, Genome Sciences Centre

amnatate

Draft genome completeness assessment using hash based approach