- 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.
- project_rm: Uploaded-dev. RM-tool. RM-tool - dev.
- new_project_rm: RM project.
- microarrays: MicroArrays Tools.
- blup_calculator: BLUP/BLUE calculator.
- xls2tabular: Xlsx sheet to tabular by name. Extract a Xlsx sheet using sheet name to a tabular dataset.
- 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.
- 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.
- bcftools_sort: Sort BCF/VCF files. Sort BCF/VCF files.
- damid_deseq2_to_bedgraph: Interpolate GATC signal from DESeq2 processed DamID data. Interpolate GATC signal from DESeq2 processed DamID data.
- package_bzlib_1_0_modified: Modified bzlib package. Modified bzlib package, with a new download link.