COVID-19 Galaxy service @EOSC-synergy

An instance of a Galaxy portal for the processing of genomic data has been setup at:

https://covid19.eosc-synergy.eu/galaxy

The portal is freely accessible and includes data on coronavirae and specially samples from SARS-CoV-2 (COVID19) daily updated from the public international databanks, as well as some key tools for identification of mutations, phylogenetic analysis, sample processing and visualization.

The portal is an open lab for researchers that want to run their experiments without the burden of downloading data and installing tools, with easy tools for sharing data, workflows and results. The backend that supports the processing of the data is jointly provided by the EOSC-SYNERGY collaboration.

Datasets available

Although every user can download its own data, the platform has already downloaded a number of collections:

  • All Coronavirus sequences from the China National Centre for Bioinformatics (CNCB) – nearly 40K sequences.
  • The collection of 961 2019-NCOV samples from China National Centre for Bioinformatics (CNCB)
  • A reference genome of the SARS-CoV-2 Wuhan-Hu-1, accession number NC_045512.2.
  • The collection of 170 SARS-CoV-2 samples from Genebank

Reference genome indexes for bwa, gatk and bowtie2 for the NC_045512.2 SARS-CoV-2 Wuhan-Hu-1, can be built.

Tools

Along with the standard tools that come with the basic installation of Galaxy, the next table shows the tools that have been installed


NameDescriptionOwnerRevision

beastBayesian MCMC analysis of molecular sequencesmalex2ca3df65222b

bowtie2Bowtie2: Fast and sensitive read alignmentdevteam749c918495f7

bwaWrapper for bwa mem, aln, sampe, and samsedevteam01ac0a5fedc3

Clustalw
ClustalW multiple sequence alignment program for DNA or proteinsdevteamd6694932c5e0

Collapse_collectionsCollection tool that collapses a list of files into a single datasset in order of appears in collectionnml830961c48e42

data_manager_bowtie_index_builderData Manager for building bowtie indexesiuc86e9af693a33

data_manager_fetch_genome_dbkeys_all_fastaAllows optionally defining a new DBKEY and retrieves a FASTA file and populate the all_fasta.loc data table.devteam4d3eff1bc421

data_manager_gatk_picard_index_builderData Manager for building gatk picard indexesdevteamb31f1fcb203c

emboss_datatypesGalaxy applicable data formats used by Emboss tools.devteama89163f31369

fastpFast all-in-one preprocessing for FASTQ filesiuc1d8fe9bc4cb0

fastqcRead QC reports using FastQCdevteame7b2202befea

fasttreeFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences – GVLiuce005e659ae21

freebayesGalaxy Freebayes Bayesian genetic variant detector tooldevteamef2c525bd8cd

gatk2
The Genome Analysis Toolkit in Version 2iuc35c00763cb5c

lofreq_callCall variants with LoFreq in Galaxy.iucdfadc322b065

lofreq_viterbiRealign reads with LoFreq in Galaxy.iucecd80c7c3886

mafftMultiple alignment program for amino acid or nucleotide sequencesrnateamc5908940967d

minimap2A fast pairwise aligner for genomic and spliced nucleotide sequencesiucb3eab4b67562

multiqcMultiQC aggregates results from bioinformatics analyses across many samples into a single reportiuc3d93dd18d9f8

nanopplotPlotting tool for long read sequencing data and alignmentsiucedbb6c5028f5

ncbi_acc_downloadDownload sequences from GenBank/RefSeq by accession through the NCBI ENTREZ APIiuc1c58de56d587

package_gatk_1_4Contains a tool dependency definition that downloads and installs version 1.4 of GATK.devteamec95ec570854

package_picard_1_56_0Contains a tool dependency definition that downloads and compiles version 1.56.0 of the Picard package.devteam99a28567c3a3

package_r_2_15_0r 2.15devteam6c34eaa82fed

package_r_ggplot2_0_9_3Contains a tool dependency definition that downloads and compiles verion 0.9.3.x from gglot2 the R package.iuc07de191649b4

package_samtools_0_1_18Contains a tool dependency definition that downloads and compiles version 0.1.18 of the SAMTools packagedevteam171cd8bc208d

package_samtools_0_1_19Contains a tool dependency definition that downloads and compiles version 0.1.19 of the SAMTools packageiucc9bd782f5342

picardPicard SAM/BAM manipulation tools.devteama1f0b3f4b781

samtool_filter2Filter BAM/SAM on FLAG,MAPQ,RG,LB or by region and produce a BAM/SAM on demanddevteam649a225999a5

samtools_fastxExtract readsiuca8d69aee190e

samtools_mpileupMPileup SNP and indel callerdevteamfa7ad9b89f4a

samtools_rmdupRemove PCR duplicatesdevteam586f9e1cdb2b

samtools_statGenerate statistics for a BAM or SAM filedevteam145f6d74ff5e

snpeffSnpEff is a genetic variant annotation and effect prediction toolboxiuc74aebe30fb52

snpsiftsnpEff SnpSift tools from Pablo Cingolaniiuc2b3e65a4252f

variant_recalibratorVariant Recalibratordevteamcb7cf57397a7

varscan_mpileupWrapper for VarScan mpileupiuce3f170cc4f95