Public Pipelines and Datasets » History » Revision 4
Revision 3 (Radhika Chippada, 06/09/2015 03:30 PM) → Revision 4/6 (Nancy Ouyang, 06/09/2015 05:21 PM)
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WARNING: WORK-IN-PROGRESS
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)