Discover bcgsc/LINKS Open Source project

Nanopore sequence read simulator

297

NanoSim

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

213

arcs

Fast hash function for DNA/RNA sequences

ntHash

🌺 reference-free transcriptome assembly for short and long reads

RNA-Bloom

🔗Genome assembly scaffolder using minimizer graphs

ntJoin

Estimating k-mer coverage histogram of genomics data

ntCard

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

biobloom

Merging, Annotation, Validation, and Illustration of Structural variants

mavis

microRNA profiling pipeline

mirna

✏️ Genome assembly polishing & SNV detection

ntEdit

Detecting multi-genome synteny using minimizer graph mapping

ntSynt

⛓ Correct misassemblies using linked AND long reads

tigmint

⛏ HLA predictions from NGS shotgun data

HLAminer

🐳 Genomics Research Container Architecture

orca

straglr

Tandem repeat expansion detection or genotyping from long-read alignments

Correct and scaffold assemblies using long reads

LongStitch

🗻 Visualization of genome/gene sequence synteny

xmatchview

de novo assembly of RNA-seq data using ABySS

transabyss

Linear-time de novo Long Read Assembler

goldrush

Platform for Oncogenomic Reporting and Interpretation (PORI)

pori

Minimizer-based assembly scaffolding and mapping using long reads

ntLink

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

RAILS

Attentive deep learning model for antimicrobial peptide prediction

AMPlify

🍶 Genome assembly with short sequence reads

SSAKE

de novo targeted gene assembly

kollector

Bioinformatics Technology Lab common code library

btllib

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

btl_bloomfilter

🔍 Post Assembly Variants Finder

pavfinder

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

chromeqc

⛓️ Construct a Physical Map from Linked Reads

physlr

Identifying repeats in high-throughput sequencing data

ntHits

Deep learning embedding for nucleotide sequences

ntEmbd

Finding putative exons and constructing splicegraphs using Trans-ABySS contigs

ChopStitch

:shipit: interactive visualization of single-cell transcriptomes

RNA-Scoop

🍼 Assemble the Genome in a Bottle sequencing data

abyss-2.0-giab

🧬 Unique (& conserved) DNA sequence identification

unikseq

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

arks

Front-end web client for the GraphKB project

pori_graphkb_client

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

pori_ipr_client

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

pori_ipr_api

JavaScript

pori_graphkb_python

Python adapter package for querying the GraphKB API

Targeted Assembly of Short Reads

TASR

Proteome Assembler with Short peptide Sequence

PASS

Visualize genome sequence assemblies

ABySS-explorer

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

pori_graphkb_loader

JavaScript

pori_ipr_python

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

Oxford nanopore transcriptome read simulator

Trans-NanoSim

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

GapPredict

Deep Neural Network model that predicts polyadenylation sites

Terminitor

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

mtGrasp

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

tasrkleat-TCGA-analysis-scripts

Jupyter Notebook

rnaseq_utils

utility scripts for RNA-seq data

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

pori_graphkb_parser

rAMPage: Rapid AMP Annotation and Gene Estimation

rAMPage

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

pori_graphkb_schema

REST API for the GraphKB project

pori_graphkb_api

JavaScript

peekseq

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

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

bloom-identity-est

ntedit_sealer_protocol

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

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

TMBur

Nextflow

goldpolish

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

GUM: Group, User Manager for LDAP

gum

dida

DIDA Project

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

sqlalchemy_hawq

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

picea-glauca-plastid

graphviz-utils

GraphViz scripts

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

qupath-annotation-exchange

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

Canadian_Biogenome_Project

Nextflow

picea-engelmannii-plastid

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

cBioportal adaptor for creating PORI reports in IPR

pori_cbioportal

🌳 Human ancestry inference from genomic data

ntRoot

Analysis scripts developed for genotyping STRs in linked-read data

link_str

command line interface for ggplot

ggcli

Utilities to assemble an organelle genome using ABySS

abyss-organelle

long_read_pog

Analysis code for a cohort of Nanopore-sequenced tumours.

tAMPer: antimicrobial peptides toxicity prediction

tAMPer

Jupyter Notebook

IMPALA

Integrated Mapping and Profiling of Allelically-expressed Loci with Annotations

lcm

Mitochondrial Genome Assembly Assessment Visualization

Mito-AssemblyViz

A pipeline for running rsem analysis on thousands of samples

rsempipeline

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

abyss-connector-paper

Stash

This repository contains the implementation for the Stash data structure

De novo antimicrobial peptide sequence generation with recurrent neural networks

AMPd-Up

🔬 Bioinformatics Technology Lab, Genome Sciences Centre

btl

Draft genome completeness assessment using hash based approach

amnatate