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in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

install_aspera_connect

Install latest version of Aspera Connect and show example how to use it for downloading sequening data.

linux-learnig-center

lofreq

LoFreq Star: Sensitive variant calling from sequencing data

lstm-human-activity-recognition

Human Activity Recognition example using TensorFlow on smartphone sensors dataset and an LSTM RNN (Deep Learning algo). Classifying the type of movement amongst six activity categories - Guillaume Chevalier

masurca

Dockerfile for the masurca assembler

metagenome

Metagenome analysis pipeline

micb405-metagenomics

A metagenome annotation workflow for UBC's Microbiology 405 course, Bioinformatics

microbialgenomemetagenomecourse

Bioinformatic course on bacterial genomics and metagenomics Helsinki December 2017

microbiomegwas

microbiomehd

Cross-disease comparison of case-control gut microbiome studies

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

miseq-16s-pipeline

HPC pipeline for overlapping V4 16S rRNA reads generated on Illumina MiSeq

ml-from-scratch

Machine Learning From Scratch. Bare bones Python implementations of Machine Learning models and algorithms with a focus on transparency and accessibility. Aims to cover everything from Data Mining to Deep Learning.

na12878

Data and analysis for NA12878 genome on nanopore

nanocorrect

Experimental pipeline for correcting nanopore reads

nanoflow

De novo assembly of nanopore reads using nextflow

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

ngs-course.github.io

NGS course

ngs-in-bioc

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

ngs2016_important_files

practice repo for github lesson at NGS 2016 course

ont-assembly-polish

ONT assembly and Illumina polishing pipeline

ordination101

Ordination lectures for Ecological Methods in Oulu

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

porechop

adapter trimmer for Oxford Nanopore reads

pydata-notebook

利用Python进行数据分析 第二版 (2017) 中文翻译笔记

pythoncode-tutorials

The Python Code Tutorials

pythondatasciencehandbook

Python Data Science Handbook: full text in Jupyter Notebooks

qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116