December 2018 Tool Shed contributions

Galaxy ToolShed

Tools contributed to the Galaxy Project ToolShed in December 2018.

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:
  • From taoufik:
  • From proteore:
  • From dereeper:
  • 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:
  • 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:
  • 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: