I. Molecular biology
II. Human genome
III. bcbio-nextgen
IV. bcbio-nextgen-vm
I am NOT a
scientist
There’s about 20 different kinds of amino acids each with their own unique shape.
GRCh38.p3 (Genome Reference Consortium Human, Build 38)
www.ensembl.org/Homo_sapiens/Location/Genome
I am P53 the protector of cells !
Who am I ?
Configuration
Variations
Insertions
Deletions
SNPs
Quality
Alignment
Coverage
Analisys
Annotations
Query
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:
More information can be found on the following link:
https://bcbio-nextgen.readthedocs.org/en/latest/contents/introduction.html
Front Node
Compute
Node
Compute
Node
Compute
Node
Messaging
Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy.
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.
"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