transPLANT Cloud Infrastructure


Available applications

Virtual Machine name

Operating System

Software installed

PMES Application / URL

COMPSs Debian (6.0.5) COMPSs (1.1.2) Generic VM to run COMPSs based applications
gene-detection Debian (6.0.5) COMPSs (1.1.2), Blast (2.2.27+), Blast2gene (2.2), GeneWise (2.0) Gene-detection (help)
Blast (help)
serial_maker+ Debian (6.0.5) Maker (2.28), Exonerate (2.2.0), Snap (2006-07-28), Augustus (2.5.5), Blast (2.2.28+), RepeatMasker (1.295), TRF (4.07b) Maker (help)
Exonerate (help)
Augustus (help)
bwapipeline Debian (6.0.5) BWA (0.1.17), bcftools (0.1.18), samtools (0.7.5a) Bwa (help)
bowtie+ Debian (6.0.5) Bowtie (2-2.2.3), tophat (2.0.12), boost (1_55), samtools boost (1_55), samtools (0.1.80.1.8) Bowtie (help)
Tophat (help)
Abyss Debian (6.0.5) Abyss (1.3.6), samtools (0.7.5a) Abyss (help)
Repet (URGI) Ubuntu (12.04.4 LTS) TEDeNovo, Blast (2.2.20 / 2.2.29+), Censor (4.2), genometools (1.5.2), Hmmer (3.1b1), MCL (12-068), Mreps (2.5), Piler (1.0), Recon (1.07), RepeatMasker (4), RepeatScout (1.0.5), Samtools (0.1.19), TRF (1.0), tRNAscan (1.23) TEdenovo (help)
Grapemine (URGI) CentOS (6.4) Intermine, Apache (2.4.10), tomcat (6.0.29), PostgreSQL (9.4) http://transplantdb.bsc.es/GrapeMine
VCF-viewer (KeyGene) Debian (6.0.5) Vcf-viewer, libZeep http://transplantdb.bsc.es/vcf-viewer
LAILAPS (IPK) Ubuntu (12.04.5 LTS) LAILAPS system, Docker (1.4.0) http://transplantdb.bsc.es/lailaps

 

Description of the applications

PMES applications allow the user to configure and launch the software installed within each cloud virtual machine. Here are detailed the arguments required by each application, the specific software used by each wrapper or pipeline, as well as the input files that each virtual machine need to access in order to run the specified software.
More detailed information about the execution process and the general I/O management can be found in the Dashboard documentation.

GENOME ANNOTATION:

MAKER

[ top ]
Application Type stand alone
This application runs the genome annotation pipeline MAKER 2.
  • MAKER: identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations.
[+/- details]

GENE DETECTION

[ top ]
Application Type COMPSs
This application is a pipeline that detects genes in a genome using a reference protein from a closely related species using Genewise. It makes the process more efficient by restricting the Genewise executions to the most relevant regions with the help of Blast and Blast2Gene.
  • GENEWISE: tool that compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. (PMID: 10779496)
  • BLAST: The Basic Local alignment tool that finds regions of local similarity between sequences.
  • BLAST2GENE: program that allows a detailed analysis of genomic regions containing completely or partially duplicated genes.
[+/- details]

AUGUSTUS

[ top ]
Application Type stand alone
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be used as an ab initio program, but the program may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
[+/- details]

TEDENOVO

[ top ]
Application Type stand alone
The application is executes TEdenovo 2.2 pipeline as included in the REPET package (https://urgi.versailles.inra.fr/)
  • TEdenovo: pipeline dedicated to detect, annotate and analyse repeats in genomic sequences, in particular, transposable elements (TEs). The pipeline starts by comparing the genome with itself using BLASTER, clusters the resulting matches with GROUPER, RECON and PILER, and for each cluster, it builds a multiple alignment from which a consensus sequence is derived. At the end, we obtain a library of classified, non-redundant consensus sequences.
[+/- details]

PAIRWISE SEQUENCE ALIGNMENT:

BLAST

[ top ]
Application Type COMPSs
This application is a wrapper of the widely used local alignment tool BLAST. The application allows the user to compose the complete command line and configure all native options.
  • BLAST: program that compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
[+/- details]

EXONERATE

[ top ]
Application Type stand alone
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using many alignment models, either exhaustive dynamic programming, or a variety of heuristics.
[+/- details]

DE NOVO ASSEMBLY

ABYSS

[ top ]
Application Type stand-alone
This application runs ABySS. The parallel version is implemented using MPI and it is capable of assembling large genomes.
  • ABYSS: de novo, parallel, paired-end sequence assembler, designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.
[+/- details]

NGS ALIGNMENT:

BWA

[ top ]
Application Type stand alone
This application is a sequential pipeline that uses BWA to align paired-end reads against a reference genome and converts the resulting alignment into a BAM file using SAM Tools.
  • BWA (Burrows-Wheeler Alignment): software package for mapping low-divergent sequences against a large reference genome.
  • SAM Tools: provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
[+/- details]

TOPHAT

[ top ]
Application Type stand alone
This application executes the TopHat program. Additionally, it runs bowtie2-build to build the genome bowtie2 indexes.
  [ bowtie2-build ] → TopHat
  • TOPHAT: is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.
The application, as the original software, behaves differently according to the given arguments. For instance:
  • Align reads: <read> <read2> <index> <cpus> <output> <options [...]>
  • Build transcriptome from GTF: <index> <cpus> <output> <options [--GTF input.gtf -- transcriptome -index newDir/prefix ...] >
  • Resume: <output> <options [--resume tophat_out] >
[+/- details]

BOWTIE

[ top ]
Application Type stand alone
This application allows launch the fast aligner Bowtie2. Additionally, the wrapper includes the option to build the indexes from input reference genomes, if the pre-build indexes of ENSEMBL Plants full-version genomes were not suitable. The application includes the following software:
   [ bowtie2-build ] → bowtie2 → samtools
  • BOWTIE2: It is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes.
  • BOWTIE2-build: The program indexes the genome with an FM Index (based on the Burrows-Wheeler Transform or BWT) to keep its memory footprint small. This step is only performed when the user supplies a genome sequence to be indexed.
  • SAM Tools: provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
[+/- details]