Sequencing Data. Paul Agapow 2011/02/03

Transcription

1 Webservices for Next Generation Sequencing Data Paul Agapow 2011/02/03

2 Aims Assumed parameters: Must have a system for non-technical users to browse and manipulate their Next Generation Sequencing (NGS) data Should be free (realistic about budget) Should be extensible and open (customization & fixing bugs) Should have permissions (security, restrictions on viewing & editing) Should be a central shared system (probably web) Prefer something with an active community Prefer something written in a sane programing language with a sane API Prefer easy setup and little administration (less work)

3 Candidates GBrowse (GMOD NGS browsing & editing tool) jbrowse (port of GBrowse) Apollo (GMOD NGS project) GMOD Drupal (integrate GBrowse into Drupal) Lookseq (NGS tool from Sanger) Galaxy (bioinformatics workflow webtool incl. NGS)

4 What is GMOD? Generic Model Organism Database A set of software components for managing, visualizing & annotating genomic data (and some other stuff) "Common" database schema (Chado) A community at Not a LIMS system

5 GBrowse A genome viewer, allowing the viewing & manipulation of annotations Navigating Zooming Selecting tracks, data sources, displayed data Can add plugins for extra functionality (e.g. Blast, alignment, search). NGS tools to show quality & depth Demo at gbrowse/c_elegans/

6 GBrowse admin & use Free and open Installs via "standard Perl module build procedure" Connectivity to various databases (and schema) via adaptors, straight CGI Import NGS data from GFF, Samtools WebGBrowse for "no config" importing Security - none

7 GBrowse pros... Big, active community, active mailing lists, used by FlyBase, WormBase A lot of different programs, (almost) all use the same schema Generic Db schema, lots of adaptors Cool functionality Proven customizable and extensible

8 GBrowse cons Goddamn Perl A Perl attitude to functionality (scripts, config files, more scripts, more config files) A Perl attitude to errors (difficult to debug) No security builtin Did I mention Perl?

9 JBrowse A port of GBrowse, being even more AJAXy-ier: "Better" Processing NGS data can take a lot of memory Still based on Perl Demo at genomes/dmel/

10 Apollo Another GMOD tool: More downstream, more for genomic data browsing & editing Java app "Currently" looking at making it a part of JBrowse

11 GMOD Drupal "module for the Drupal CMS which simplifies programming bioinformatic Drupal modules" Implements subset of Chado Can make datasets private or public, select users for access Support for HPC (Condor) Users can upload FASTA files to act as query or database "Active"? (CSIRO supported) (Still using Perl underneath) More for blast and alignment than NGS

12 Lookseq "JavaScript-based viewer for DNA sequencing read alignments", "browsing and analysis of genome sequence data" technology agnostic emphasize browsing & zooming can see SNPs and depth and so on Visualize heterogenity Uses "basic SQL" Can directly uses SAM/BAM

13 Lookseq but... Extensible, but not actually extended? Documents & pages in some disarray (abandonware?) Frakking Perl

14 Galaxy "Genome analysis platform" Workflows (see next slide) A proper permission system: users, groups, datasets!, roles Python Download and run installation Part of GMOD?

15 Galaxy workflows Self-describing analyses and workflows History Non-destructive Can connect external datasources (and datatypes) Can function asynchronously Can use HPC Well-defined tool API

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17 Galaxy tools To create a Galaxy tool: 1. Make a directory in ``galaxy/ tools`` 2. Make a configuration file 3. Add tool to Galaxy registry file 4. Restart Galaxy <tool id="fa_gc_content_1" name="compute GC content">! <description>for each sequence in a file</description>! <command interpreter="perl">toolexample.pl $input $output<! <inputs>!! <param format="fasta" name="input" type="data" label=! </inputs>! <outputs>!! <data format="tabular" name="output" />! </outputs>! <help>this tool computes GC content from a FASTA file.</he </tool> Can also add datatypes, data sources and visualizations

18 Galaxy for NGS "Tools" are wrappers around external, pre-existing software (dependency hell?) E.g. Bowtie, BWA, LASTZ, Megablast, SRMA, SAMtools Fastq as a lingua franca More of an integration and browsing tool than editing? Mainly reference mapping They sure do love them screencasts

19 Conclusions For usuability, if you can bear no access restrictions and using Perl: Lookseq or JBrowse. For extensibility, if a stepwise "tools" approach will do, and you can ask a little more of users: Galaxy. For rolling your own, if you have the time: use JBrowse code for UI.