Cloud Infrastructure Applications

human, fly, arabidopsis, brugia, aedes, tribolium, schistosoma, tetrahymena, galdieria, maize, toxoplasma, caenorhabditis, , aspergillus_fumigatus, aspergillus_nidulans, aspergillus_oryzae, aspergillus_terreus, botrytis_cinerea, candida_albicans, candida_guilliermondii, candida_tropicalis, chaetomium_globosum, coccidioides_immitis, coprinus, coprinus_cinereus, cryptococcus_neoformans_gattii, cryptococcus_neoformans_neoformans_B, cryptococcus_neoformans_neoformans_JEC21, debaryomyces_hansenii, encephalitozoon_cuniculi_GB, eremothecium_gossypii, fusarium_graminearum, histoplasma_capsulatum, kluyveromyces_lactis, laccaria_bicolor, lamprey, leishmania_tarentolae, lodderomyces_elongisporus, magnaporthe_grisea, neurospora_crassa, phanerochaete_chrysosporium, pichia_stipitis, rhizopus_oryzae, saccharomyces_cerevisiae_S288C, saccharomyces_cerevisiae_rm11-1a_1, schizosaccharomyces_pombe, trichinella, ustilago_maydis, yarrowia_lipolytica, nasonia, tomato, chlamydomonas, amphimedon, pneumocystis

Consult http://augustus.gobics.de/binaries/README.TXT to modify the default parameter or add others.

Are also available though the shared storage, the Plant Esembl genomes (release 20) and the GRCh37 human genome. In order to use them, specify one of the following options:

Default: –model ungapped –bestn 0 –score 100 –exhaustive FALSE –showtargetgff yes

-1 : Bowtie2 indexes basename. The program will look index*bt2 and index*rev.bt2 files, which require to be uploaded (Input tab).

-2: comma-separated list of files containing reads in FASTA format. They will be indexed using Bowtie2-build program.

Check options at: http://ccb.jhu.edu/software/tophat/manual.shtml

When using pre-built indexes in ‘index’, *.1.bt2 and *.rev.1.bt2 files need to be uploaded. When new indexes are to be build, the original genomic FASTA files should be transfered.

Additionally, when user supplies their own insertions, deletions, or list of known transcripts, the corresponding .GTF, .BED, .JUNCS, etc., files need to be correclty specified within ‘TopHat options’, as well as uploaded through the ‘input’ tab.

When a new transcriptome index is created ( –GTF & –transcriptome-index within ‘TopHat options’), it is included in the [OUTPUT].tar.gz, so it can be reused in other TopHat runs.

1. genome sequence : comma-separated list of FASTA files containing the reference sequences to be aligned to. From them, FM indexes will be created running bowtie2-build program.
2. genome index: base-name of the index of a pre-build reference genome. The base-name is the name of any of the index files up to but not including the final *.1.bt2, *.rev.1.bt2, etc. User can upload their own index files, or use those available in the shared disk. Following are the basenames of the pre-build genomes:

arabidopsis_lyrata arabidopsis_thaliana brachypodium_distachyon brassica_rapa chlamydomonas_reinhardtii cyanidioschyzon_merolae glycine_max

hordeum_vulgare medicago_truncatula musa_acuminata oryza_brachyantha oryza_glaberrima oryza_indica oryza_indica

oryza_sativa physcomitrella_patens populus_trichocarpa selaginella_moellendorffii setaria_italica solanum_lycopersicum solanum_tuberosum

sorghum_bicolor triticum_aestivum triticum_urartu vitis_vinifera zea_mays

Default: -f –offrate 5

Default: –end-to-end –sensitive –un-gz unpaired.sam.gz –met-file metrics.log –time

The target name or target path (3th column) should correspond to the argument ‘read’ and ‘read_2’.

Additionally, when user supplies their own indexes, all *.1.bt2 and *.rev.1.bt2 files need to be uploaded, and their path and base-names set in the argument ‘reference’. However, if ‘reference’ argument refers to genomic sequences, the files to upload are the FASTA reference genome sequences.

It will contain a variable number of files, created according to the provided options:

• indexes files (reference*.bt2 and reference.rev.*.bt2 )
• SAM and BAM read’s alignments (alignment.sam, alignment.bam)
• file containing unpaired reads that fail to align (named according to –un options)
• file containing unpaired reads that align at least once (named according to –al options)
• file containing paired-end reads that fail to align concordantly (named according to –un-conc options)
• file containing paired-end reads that align concordantly at least once to file (named according to –al-conc options)
• bowtie2 metrics file (named according to –metrics-file)