Public Pipelines and Datasets » History » Revision 2
Revision 1 (Nancy Ouyang, 03/20/2015 07:12 PM) → Revision 2/6 (Nancy Ouyang, 03/28/2015 05:26 AM)
{{>toc}} WARNING: WORK-IN-PROGRESS h1. Public Pipelines Bcbio-nextgen -- 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 -- 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: 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 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 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 h1. Public Datasets