References¶

Software required by amplimap¶

  • pysam: https://github.com/pysam-developers/pysam [MIT]
  • biopython: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp163 [BSD-3]
  • pandas: “Wes McKinney. Data Structures for Statistical Computing in Python, Proceedings of the 9th Python in Science Conference, 51-56 (2010)” [BSD-3]
  • Snakemake: http://bioinformatics.oxfordjournals.org/content/28/19/2520 [MIT]
  • samtools: https://www.ncbi.nlm.nih.gov/pubmed/19505943 [MIT]
  • bedtools: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832824/ [GPL]
  • UMI-tools: http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract [MIT]
  • pyfaidx: https://peerj.com/preprints/970/ [BSD-3]

Recommended additional software¶

  • BWA: https://arxiv.org/abs/1303.3997
  • Bowtie2: https://www.nature.com/articles/nmeth.1923
  • STAR: https://academic.oup.com/bioinformatics/article/29/1/15/272537
  • Platypus: http://www.nature.com/ng/journal/v46/n8/full/ng.3036.html
  • GATK: https://www.nature.com/articles/ng.806
  • Annovar: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938201/

amplimap

Navigation

  • Installation
  • Quickstart
  • Input and the working directory
  • Running amplimap
  • Output: the analysis directory
  • Configuration
  • Tutorials
  • Advanced usage
  • Extended installation guide for amplimap
  • Code documentation
  • References
    • Software required by amplimap
    • Recommended additional software

Related Topics

  • Documentation overview
    • Previous: Code documentation

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