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ToolShed/Contributions/2015_05

May 2015 Tool Shed Contributions

Tools contributed to the Galaxy Project Tool Shed in May 2015.

In no particular order:

Tools

  • From biotechcoder:

    • riboseqr_wrapper: Wrapper for riboSeqR (R package) riboSeqR is an R/Bioconductor package for the analysis of sequencing data from ribosome profiling experiments. This tool is a Galaxy wrapper for riboSeqR.

  • From lxue:

    • ageseq: Perl code Analysis of Genome Editing by Sequencing AGEseq compares amplicon sequences with expected target sequences and finds the insertion/deletion sites in the amplicon sequences. Please refer to this document for more details.
      http://aspendb.uga.edu/AGEseq/AGEseq_Readme.docx

  • From mvdbeek:

    • mismatch_frequencies: planemo upload for repository https://bitbucket.org/drosofff/gedtools/ calculate mismatch frequencies for individual nucleotide mismatches Given a set of aligned reads in BAM/SAM format, calculates and plots the frequency of all possible nucleotide mismatches with respect to the reference sequence.

  • From rnateam:

    • dorina: data source for RNA interactions in post-transcriptional regulation The expression of almost all genes in animals is subject to post-transcriptional regulation by RNA binding proteins (RBPs) and microRNAs (miRNAs). The interactions between both RBPs and miRNAs with mRNA can be mapped on a whole-transcriptome level using experimental and computational techniques.
      doRiNA is a RESTful webservice that collects data from such experiments.

    • antarna: planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit 71414cf7f040d610afc3f02be31446efc3a82a40-dirty antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .

  • From proteomisc:

    • gcms_lcms_analysis: GCMS and LCMS workflows Tools for Proteomics analysis , preprocessing , exploratory analysis and visualization for GCMS and LCMS protocols

  • From iuc:

    • vsearch: VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. Open and free 64-bit multithreaded tool for processing metagenomic sequences, including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling.

      https://github.com/torognes/vsearch

    • jbrowse: planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e JBrowse static site generator JBrowse is a fast, extensible JS+HTML5 genome browser. This tools allows you to visualise GFF, BED, and other data directly in Galaxy with JBrowse

    • hmmer3: planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 HMM based sequence alignment and database search tool HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

      http://hmmer.janelia.org/

    • package_stringtie_1_0_3: planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_0_3 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 Contains a tool dependency definition that downloads and installs version 1.0.3 of the stringtie RNA-seq assembler. StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

    • rgrnastar: planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef RNA STAR 2.4 WARNING! This will eat all your cluster node RAM and then some.

      hg19 uses about 30GB but it's really fast. See http://gettinggeneticsdone.blogspot.com.au/2012/11/star-ultrafast-universal-rna-seq-aligner.html<<BR>><<BR>>You also need a new set of genome indexes. Sigh. So you have to build those yourself until I figure out how to make an index manager.

      Most of this wrapper was originally written by Jeremy Goecks, with kibbitzing and automated dependency installation by Ross Lazarus.

  • From jeremyjliu:

    • region_motif_data_manager: Installs motif databases and reference files for use with region_motif_enrichment. Companion data manager to region_motif_enrichment. Installs motif databases in tabix format and reference motifs in meme format that are provided as standard databases for region_motif_enrichment.

  • From geert-vandeweyer:

    • multiplicom_primer_trimming: trim Multiplicom primer sequences from paired FastQ files Tool uses MASTR assay design files to remove primer sequences from the raw fastq files.

  • From insilicosolutions:

    • cravat: Annotates mutations with CRAVAT Mutations in hg19 genomic coordinates can be annotated with CRAVAT (Cancer-Related Analysis of VAriants Toolkit). Annotations include VEST mutation pathogenicity score, COSMIC, dbSNP, allele frequencies (1000 Genomes, ESP6500, and ExAC), mappability warnings, TARGET (tumor alterations relevant for genomics-driven therapy), PubMed, and mapping to 3D-structures.

  • From yhoogstrate:

  • From devteam:

    • gffread: planemo upload commit a52cc16ed8d0d60e99742b55fccbdedcbb64b82c cufflinks gffread filters and/or converts GFF3/GTF2 records cufflinks gffread filters and/or converts GFF3/GTF2 records and can produce cdna, CDS, peptide fasta sequences

    • data_manager_picard_index_builder: planemo upload commit e4c87b7392ace0d6ac5ba2d926e1dd176f987985 data_manager_picard_index_builder data_manager_picard_index_builder

  • From drosofff:

fasta and fastq output

  • From rekado:

    • dorina: initial tool definition. Definition for DoRiNA data source This tool makes it possible to send tabular results obtained from a DoRiNA search to a Galaxy instance.

Dependency Definitions

  • From iuc:

    • package_bowtie_2_2_5: Contains a tool dependency definition that downloads and compiles version 2.2.5 of the Bowtie package Contains a tool dependency definition that downloads and compiles version 2.2.5 of the Bowtie package

    • package_tophat_2_0_14: Contains a tool dependency definition that downloads and compiles version 2.0.14 of TopHat2. TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

    • package_augustus_3_1: Contains a tool dependency definition that downloads and compiles version 3.1 of Augustus AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.

      http://bioinf.uni-greifswald.de/augustus/

  • From geert-vandeweyer:

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