Arvados

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h1. Public Pipelines

h2. Bcbio-nextgen

By: Brad Chapman

Bcbio-nextgen is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

p(. Source Documentation: https://bcbio-nextgen.readthedocs.org/en/latest/

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/Bcbio-nextgen_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-a45rn6qhjszct1d

h2. GATK 2 Unified Genotyper

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. Raw reads are processed and the GATK UnifiedGenotyper is will call SNPs and indels.

p(. Source Documentation: http://gatkforums.broadinstitute.org/discussion/17/gatk-2-0-announcement

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/GATK2_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-iodpr5gc65cp4t0

h2. GATK 3 Haplotype Caller

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. Raw reads are processed then, the GATK HaplotypeCaller will call SNPs and indels simultaneously via local re-assembly of haplotypes in an active region.

p(. Source Documentation: https://www.broadinstitute.org/gatk/blog?tag=gatk3

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/GATK3_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-l1emsbyyx6wyjdh

h2. lobSTR 3

lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.

p(. Source Documentation: http://melissagymrek.com/lobstr-code/

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/LobSTR_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-up6qgpqz5ie2vfq

h2. Platypus

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb.

p(. Source Documentation: http://www.well.ox.ac.uk/platypus

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/Platypus_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-xcntt7rtz251isk

h2. Pathomap -- Ancestry Mapper

By: Chris Mason

PathoMap is a research project by Weill Cornell Medical College to study the microbiome and metagenome of the built environment of NYC. The Ancestry Mapper pipeline is one pipeline out of the Pathomap suite, which takes human high-throughput sequencing data and creates an ancestry map.

p(. Source Documentation: http://www.pathomap.org/about/

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/pathomap_tutorial/

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-662ij1pcw6bj8uj

h2. Tuxedo Suite (BTC)

The Tuxedo Suite (Bowtie, Tophat, Cufflinks) takes High-throughput RNA sequencing data and assembles transcripts and estimates their relative abundances, without using a reference annotation.

p(. Source Documentation:

p(((. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

p(((. http://ccb.jhu.edu/software/tophat/index.shtml

p(((. http://cole-trapnell-lab.github.io/cufflinks/

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/Tuxedo_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-ziejtm5kaik7ndl

h2. VCF-compare

Compares positions in two VCF files and outputs concordance and discordance rates.

p(. Source Documentation: http://vcftools.sourceforge.net/perl_module.html#vcf-compare

p(. Arvados Documentation: https://arvados.org/projects/arvados/wiki/Vcf-compare_tutorial

p(. Link to Arvados Project: https://workbench.qr1hi.arvadosapi.com/projects/qr1hi-j7d0g-qhf708xb2s7cow2

h2. All the tutorials

Each of the following tutorials introduces the following Arvados features:

* How to run the pipeline using Arvados

* How to access your pipeline results

* How to browse and select your input data for lobSTR and submit re-run the pipeline

p(. https://arvados.org/projects/arvados/wiki/Platypus_tutorial

p(. https://arvados.org/projects/arvados/wiki/gatk2_tutorial

p(. https://arvados.org/projects/arvados/wiki/gatk3_tutorial

p(. https://arvados.org/projects/arvados/wiki/bcbio-nextgen_tutorial

p(. https://arvados.org/projects/arvados/wiki/Tuxedo_tutorial

p(. https://arvados.org/projects/arvados/wiki/Pathomap_tutorial

h1. Public Datasets (TBD)