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