README 3.3 KB

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  1. Unipro UGENE is a multiplatform open-source software with the main
  2. goal of assisting molecular biologists without much expertise in
  3. bioinformatics to manage, analyze and visualize their data.
  4. UGENE integrates widely used bioinformatics tools within a common user
  5. interface. The toolkit supports multiple biological data formats and
  6. allows the retrieval of data from remote data sources. It provides
  7. visualization modules for biological objects such as:
  8. - annotated genome sequences
  9. - Next Generation Sequencing (NGS) assembly data
  10. - multiple sequence alignments
  11. - phylogenetic trees
  12. - 3D structures
  13. Most of the integrated algorithms are tuned for maximum performance by
  14. the usage of multithreading and special processor instructions. UGENE
  15. includes a visual environment for creating reusable workflows that can
  16. be launched on local resources or in a High Performance Computing
  17. (HPC) environment. UGENE is written in C++ using the Qt framework. The
  18. built-in plugin system and structured UGENE API make it possible to
  19. extend the toolkit with new functionality.
  20. CITING:
  21. Unipro UGENE: a unified bioinformatics toolkit
  22. Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
  23. Bioinformatics 2012 28: 1166-1167
  24. EXTERNAL TOOLS
  25. UGENE can use and drive a number of external tools, providing a nice
  26. and unified GUI. These are not needed at build time, but are highly
  27. recommended for the complete (and extended) functionality of the
  28. program. All of them are available at SlackBuilds.org:
  29. - bedGraphToBigWig (Convert bedGraph to bigWig file)
  30. - bedtools (A powerful toolset for genome arithmetic)
  31. - bowtie (A short read aligner of DNA sequences)
  32. - bowtie2 (A tool for aligning sequencing reads)
  33. - bwa (Burrows-Wheeler Aligner)
  34. - cap3 (CAP3: A DNA sequence assembly program)
  35. - cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
  36. - cistrome-conductGO (Find the top-n highest expressed TFs)
  37. - cistrome-extra (Cistrome Applications Harvard extra apps)
  38. - cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
  39. - cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
  40. - clark-ugene (Ugene's forked CLAssifier based on Reduced K-mers)
  41. - clustalo (Clustal Omega)
  42. - clustalw (Multiple Sequence Alignment)
  43. - cufflinks (A reference-guided assembler for RNA-Seq experiments)
  44. - cutadapt (Trim adapters from high-throughput sequencing reads)
  45. - diamond (A sequence aligner for protein and translated DNA)
  46. - fastqc (A quality control tool for high throughput sequence data)
  47. - HMMER (Biosequence analysis using profile hidden Markov models)
  48. - kraken (Assign taxonomic labels to short DNA sequences)
  49. - MetaPhlAn (Metagenomic Phylogenetic Analysis)
  50. - ncbi-blast (BLAST: Basic Local Alignment Search Tool)
  51. - ncbi-blast+ (BLAST+ Command Line Applications)
  52. - PhyML (Phylogenetic estimation using Maximum Likelihood)
  53. - samtools-legacy (Sequence Alignment/Map Tools)
  54. - snpEff (Genetic variant annotation and effect prediction toolbox)
  55. - spades (SPAdes Genome Assembler)
  56. - spidey (mRNA-to-genomic alignment)
  57. - t_coffee (A multiple sequence alignment program)
  58. - tabix-legacy (Generic indexer for TAB-delimited genome position files)
  59. - tophat (Splice junction mapper for RNA-Seq reads)
  60. - trimmomatic (A flexible read trimming tool for Illumina NGS data)
  61. - vcftools (A program package designed for working with VCF files)
  62. Alternatively, check the program's website if you want to get them
  63. precompiled.