Metagenomics tools & workflows Galaxy Hackathon 2015
#galhackmetafr Brest Ifremer Rennes INRIA IRISA INRA CNRS U. Rennes1 Toulouse INRA Clermont-Ferrand CIDAM U. Auvergne INRA Gif/Yvette IFB Core Metagenomics Galaxy Hackathon, 30/11 & 1/ Remote hackathon links
-Official page -Mothur -Qiime Github links GUGGO dedicated pages : Remote hackathon dedicated page
Public: https://cesgo.genouest.org/groups/guggo/wiki/MEtagenomicsHackathon Private: https://cesgo.genouest.org/projects/galhackmetafr/notes/ Remote hackathon dedicated page https://github.com/galaxyproject/tools-iuc/issues/299 Mothur dedicated page https://github.com/galaxyproject/tools-iuc/issues/419 Qiime No dedicated page, see on https://github.com/galaxyproject/tools-iuc/issues/299 Peter Briggs Lance Parsons Metagenomics Pipelines
OTU research Find Rapidly OTUs with Galaxy Solution
FROGS Pipeline (from Escudi et al. Galaxy day 2015) Workflow execution time: ~11h from 9,6 Millions MiSeq reads Find Rapidly OTUs with Galaxy Solution
FROGS Pipeline (from Escudi et al. Galaxy day 2015) Find Rapidly OTUs with Galaxy Solution
FROGS Pipeline (from Escudi et al. Galaxy day 2015) Find Rapidly OTUs with Galaxy Solution
FROGS Pipeline (from Escudi et al. Galaxy day 2015) Mothur 1.32 based easyOTU easyOTU SFF to Fasta Fasta to OTU list
OTU and sequence classification OTU to graph Input : 454 data Workflow execution time: ~10h for 1 Million 454 reads Mothur 1.32 based easyOTU easyOTU SFF to Fasta Mothur 1.32 based easyOTU easyOTU Fasta2OTU Mothur 1.32 based easyOTU easyOTU Fasta2OTU Duplicates discovery Mothur 1.32 based easyOTU easyOTU Minepy ASaiM easyOTU TOOLshedization Enhance exchange & automatic installation Tools FROGS tools ASaiM tools DOCKERization Enhance reproducibility & exchange Tools Swarm Vsearch Cutadapt Flash RDPClassifier .. Results Public pages Dedicated GUGGO wiki page
Trello : https://trello.com/b/M0jf4MIh/hackathon-galaxy-metagenomics Github repos FROGS: https://github.com/geraldinepascal/FROGS Dependencies: https://github.com/fescudie/frogs-dependencies FROGS Docker: https://github.com/fescudie/frogs-docker IUC Contribution Fest Metagenomics Tools & Workflows IUC Qiime: https://github.com/galaxyproject/tools-iuc/issues/426 IUC Mothur: https://github.com/galaxyproject/tools-iuc/issues/419 Swarm package: https://github.com/galaxyproject/tools-iuc/pull/435 Flash: https://github.com/galaxyproject/tools-iuc/issues/441 Public pages Github repos Docker:
RDPTools: https://github.com/cmonjeau/docker_rdptools FLASH: https://github.com/cmonjeau/docker_flash Vsearch: https://github.com/cmonjeau/docker_vsearch SWARM: https://github.com/cmonjeau/docker_swarm FROGS Docker: Clustering: https://github.com/fescudie/frogs-docker/tree/master/clustering Preprocess: https://github.com/fescudie/frogs-docker/tree/master/preprocess Remove_chimera: https://github.com/fescudie/frogs-docker/tree/master/remove_chimera Biom_to_stdbiom: https://github.com/sandrineperrin/dockerfiles/tree/create_some_tools/biom_to_stdbiom/biom_to_stdbiom_1.1.1 Biom_to_tsv: https://github.com/sandrineperrin/dockerfiles/tree/create_some_tools/biom_to_tsv/biom_to_tsv_2.1.0 Clusters_stat: https://github.com/sandrineperrin/dockerfiles/tree/create_some_tools/clusters_stat/clusters_stat_1.1.0 Demultiplex: https://github.com/sandrineperrin/dockerfiles/tree/create_some_tools/demultiplex/demultiplex_1.1.0 Filters: https://github.com/sandrineperrin/dockerfiles/tree/create_some_tools/filters/filters_1.2.0 Upload_tar: https://github.com/sandrineperrin/dockerfiles/tree/create_some_tools/upload_tar/upload_tar_0.1.1 Public pages Github repos
Tool integration Guidelines: https://github.com/galaxy-iuc/standards/issues/24 Toolshedization Diamond: https://github.com/galaxyproject/tools-iuc/pull/428#issuecomment PRINSEQ: https://github.com/galaxyproject/tools-iuc/issues/444 SortMeRNA: https://github.com/ASaiM/galaxytools-1/tree/sortmerna_wrapper_upgrade Misc Enhance fun!