Alexandru Coman

Cloud Engineer @Cloudbase

 Teaching Assistant @FII

 

www.alexcoman.com

A briefer history of

bcbio-nextgen(-vm)

I.   Molecular biology

II.  Human genome

III. bcbio-nextgen

IV. bcbio-nextgen-vm

Table of content

Disclaimer

I am NOT a

scientist

I. Amino Acids

There’s about 20 different kinds of amino acids each with their own unique shape.

II. Human genome

GRCh38.p3 (Genome Reference Consortium Human, Build 38)

www.ensembl.org/Homo_sapiens/Location/Genome

II. Mutation

I am P53 the protector of cells !

Who am I ?

II. Time to solve some diseases

Configuration

Variations

Insertions

Deletions

SNPs

Quality

Alignment

Coverage

Analisys

Annotations

Query

III. bcbio-nextgen

III. Utilities

bedtools, bcftools, biobambam, sambamba, samblaster, samtools, vcflib 

Aligners:

bwa-men, novoalign, bowtie2

Variantion:

FreeBayes, GATK, Platypus, MuTecT, scalpel, SnpEff, VEP, GEMINI, Lumpy, Delly

RNA-seq:

Tophat, STAR, cufflinks, HTSeq

Quality control:

fastqc, bamtools, RNA-SeQC

Manipulation:

III. Users

  • Harvard School of Public Health
  • Massachusetts General Hospital
  • Science for Life Laboratory
  • Institute of Human Genetics, UCSF
  • IRCCS “Mario Negri” Institute for Pharmacological Research
  • The Translational Genomics Research Institute (TGen)
  • Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT

 

More information can be found on the following link:

https://bcbio-nextgen.readthedocs.org/en/latest/contents/introduction.html

III. How to run it ?

bcbio-nextgen-vm

IV. Elasticluster

Front Node

Compute

Node

Compute

Node

Compute

Node

Messaging

IV.                    

Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy. 

IV. Docker

Docker containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries - anything you can install on a server.

IV. SLURM

"My general thoughts are that this is an exciting time to contribute to open source work in bioinformatics.

This will enable individuals to learning more about their genetics and tailor their lifestyles and disease management. In terms of open source bioinformatics research, this means we'll have an increasing pool of individuals interested in being able to analyze their own genomes.

We hope that this will enable everyone to investigate their own genomes and build a large community of both professional and amateur scientists."

Brad Chapman

Research Associate, Bioinformatics Core la Harvard School of Public Health

Questions !?

Resources

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