Take Home Message
• NGS data analyses are computationally intensive.
• Bioconda is a channel for the Conda package manager specializing in bioinformatics software.
• To run other NGS data analysis tools not installed via conda set the path to the
executable files in your *.bashrc.
Further Reading The Biostar Handbook: 2nd Edition.
https://www.biostarhandbook.com/.
Acknowledgements We thank Patricia Basurto and Carolina Castañeda ot the International Laboratory for Human Genome Research (National Autonomous University of Mexico, Juriquilla campus) for reviewing this chapter.
References
1. Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT. BamTools: a C++ API and
toolkit for analyzing and managing BAM files. Bioinformatics. 2011;27(12):1691–2.
2. Danecek P, McCarthy SA. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics.
2017;33(13):2037–9.
3. Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, Durbin R. BCFtools/RoH: a hidden
Markov model approach for detecting autozygosity from next-generation sequencing data.
Bioinformatics. 2016;32(11):1749–51.
4. Quinlan AR. BEDTools: The Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11 2 1–34.
5. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 2010;26(6):841–2.
6. Langdon WB. Performance of genetic programming optimised Bowtie2 on genome comparison
and analytic testing (GCAT) benchmarks. BioData Min. 2015;8(1):1.
7. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.
Bioinformatics. 2010;26(5):589–95.
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009;25(14):1754–60.
9. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite.
Trends Genet. 2000;16(6):276–7.
10. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements.
Nat Methods. 2015;12(4):357–60.
11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map
format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
12. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B
cell identities. Molecular Cell. 2010;38(4):576–89.
68
M. Kappelmann-Fenzl
• NGS data analyses are computationally intensive.
• Bioconda is a channel for the Conda package manager specializing in bioinformatics software.
• To run other NGS data analysis tools not installed via conda set the path to the
executable files in your *.bashrc.
Further Reading The Biostar Handbook: 2nd Edition.
https://www.biostarhandbook.com/.
Acknowledgements We thank Patricia Basurto and Carolina Castañeda ot the International Laboratory for Human Genome Research (National Autonomous University of Mexico, Juriquilla campus) for reviewing this chapter.
References
1. Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT. BamTools: a C++ API and
toolkit for analyzing and managing BAM files. Bioinformatics. 2011;27(12):1691–2.
2. Danecek P, McCarthy SA. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics.
2017;33(13):2037–9.
3. Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, Durbin R. BCFtools/RoH: a hidden
Markov model approach for detecting autozygosity from next-generation sequencing data.
Bioinformatics. 2016;32(11):1749–51.
4. Quinlan AR. BEDTools: The Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11 2 1–34.
5. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 2010;26(6):841–2.
6. Langdon WB. Performance of genetic programming optimised Bowtie2 on genome comparison
and analytic testing (GCAT) benchmarks. BioData Min. 2015;8(1):1.
7. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.
Bioinformatics. 2010;26(5):589–95.
8. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009;25(14):1754–60.
9. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite.
Trends Genet. 2000;16(6):276–7.
10. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements.
Nat Methods. 2015;12(4):357–60.
11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map
format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
12. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B
cell identities. Molecular Cell. 2010;38(4):576–89.
68
M. Kappelmann-Fenzl