References
----------

Software required by amplimap
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-  pysam: https://github.com/pysam-developers/pysam [`MIT <https://github.com/pysam-developers/pysam/blob/master/htslib/LICENSE>`_]
-  biopython: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp163 [`BSD-3 <https://github.com/biopython/biopython/blob/master/LICENSE.rst>`_]
-  pandas: “Wes McKinney. Data Structures for Statistical Computing in
   Python, Proceedings of the 9th Python in Science Conference, 51-56
   (2010)” [`BSD-3 <https://pandas.pydata.org/pandas-docs/stable/overview.html#license>`_]
-  Snakemake: http://bioinformatics.oxfordjournals.org/content/28/19/2520 [`MIT <http://snakemake.readthedocs.io/en/stable/project_info/license.html>`_]
-  samtools: https://www.ncbi.nlm.nih.gov/pubmed/19505943 [`MIT <https://github.com/samtools/samtools/blob/develop/LICENSE>`_]
-  bedtools: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832824/ [`GPL <https://github.com/arq5x/bedtools/blob/master/LICENSE>`_]
-  UMI-tools: http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract [`MIT <https://github.com/CGATOxford/UMI-tools/blob/master/LICENSE>`_]
-  pyfaidx: https://peerj.com/preprints/970/ [`BSD-3 <https://github.com/mdshw5/pyfaidx/blob/master/LICENSE>`_]

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
-  weCall: https://github.com/Genomicsplc/wecall
-  Annovar: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938201/