Public Pipelines¶

Bcbio-nextgen¶

By: Brad Chapman

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

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

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

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

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.

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

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

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

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.

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

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

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

lobSTR 3¶

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

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

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

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

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.

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

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

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

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.

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

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

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

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.

Source Documentation:

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

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

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

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

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

VCF-compare¶

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

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

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

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

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

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

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

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

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

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

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