December 2018 Tool Shed contributions

Tools contributed to the Galaxy Project ToolShed in December 2018.

• All monthly summaries

New Tools

• From iuc:

  • mummer_mummerplot: Wrapper for the MUMmer4 tool: Mummerplot. MUMmer is a system for rapidly aligning entire genomes. The current version (release 4.x) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer.
  • mummer_show_coords: Wrapper for the MUMmer4 tool: Show-Coords.
  • mummer_mummer: Wrapper for the MUMmer4 tool: Mummer.
  • mummer_dnadiff: Wrapper for the MUMmer4 tool: DNAdiff.
  • mummer_delta_filter: Wrapper for the MUMmer4 tool: Delta-Filter.
  • mummer_nucmer: Wrapper for the MUMmer4 tool: Nucmer.

• From gianmarco_piccinno:

  • project_rm: Uploaded-dev. RM-tool. RM-tool - dev.

• From fabio:

  • new_project_rm: RM project.

• From taoufik:

  • microarrays: MicroArrays Tools.

• From proteore:

  • proteore_heatmap_visualization: Build an heatmap from an uto table.
  • proteore_maps_visualization: map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.

• From dereeper:

  • blup_calculator: BLUP/BLUE calculator.

• From ylebras:

  • xls2tabular: Xlsx sheet to tabular by name. Extract a Xlsx sheet using sheet name to a tabular dataset.

• From mingchen0919:

  • aurora_deseq2: Differential expression analysis with R DESeq2 package.
  • aurora_star: ultrafast universal RNA-seq aligner.
  • aurora_htseq_site: Counting reads in features.
  • aurora_fastqc: Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads files.
  • aurora_skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
  • aurora_htseq: Counting reads in features.
  • aurora_skewer_site: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads.

• From thomaswollmann:

  • points2labelimage: Points to label image. Converts points to label image.
  • labelimage2points: Label Image to Points. This tool converts a label image to points.
  • detection_viz: Detection Visualization. This tool visualizes detection.

• From bitlab:

  • imsame: A Pairwise Incremental Multi-Staged Alignment Method for Metagenomes Comparison. IMSAME (Incremental Multi-Stage Alignment of MEtagenomes) is a tool for the exhaustive pairwise metagenomic analysis. This tool offers a high-level of sensitivity which makes it able to discover low conserved signals.
  • gecko: A pairwise genome comparison software for the detection of High-scoring Segment Pairs. The comparison of genomes is a traditional problem with high memory and CPU time requisites. Those requisites can be reduced redesigning the process and using HPC techniques in its development. We have developed a program for genomes comparison handling long sequences.
  • chromeister: A heuristic approach for ultra fast previsualization of pairwise genome comparisons. A heuristic approach for ultra fast previsualization of pairwise genome comparisons.

• From greg:

  • bcftools_sort: Sort BCF/VCF files. Sort BCF/VCF files.

• From mvdbeek:

  • damid_deseq2_to_bedgraph: Interpolate GATC signal from DESeq2 processed DamID data. Interpolate GATC signal from DESeq2 processed DamID data.

• From si-datascience:

  • package_bzlib_1_0_modified: Modified bzlib package. Modified bzlib package, with a new download link.