11. Bibliography

BAMTOOLS

https://github.com/pezmaster31/bamtools

BCFTOOLS

http://www.htslib.org/doc/bcftools.html

BEDTOOLS

BEDTools: a flexible suite of utilities for comparing genomic features Aaron R. quinlan, Ira M. Hall 2010 Bioinformatics 26(6) https://doi.org/10.1093/bioinformatics/btq033

BIOPYTHON

Biopython: freely available Python tools for computational molecular biology and bioinformatics. Cock et al 2009, Bioinformatics 25(11) https://doi.org/10.1093/bioinformatics/btp163

DEEPTOOLS

Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. “deepTools2: a next generation web server for deep-sequencing data analysis.” Nucleic Acids Research (2016): gkw257.

DSRC

https://github.com/refresh-bio/DSRC

GOALIGN

https://github.com/evolbioinfo/goalign

GOTREE

https://github.com/evolbioinfo/gotree

MOSDEPTH

Mosdepth: quick coverage calculation for genomes and exomes Brent S Pedersen, Aaron R Quinlan 2018 Bioinformatics, 34(5) https://doi.org/10.1093/bioinformatics/btx699

PANDAS

Wes McKinney. Data Structures for Statistical Computing in Python, Proceedings of the 9th Python in Science Conference, 51-56 (2010)

PIGZ

https://zlib.net/pigz/

http://zzz.bwh.harvard.edu/plink/

PYEXCEL

http://docs.pyexcel.org/en/latest/

PYSAM

The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8. PMID: 19505943

SAMBAMBA

https://lomereiter.github.io/sambamba/

SAMTOBAM

Ogasawara T, Cheng Y, Tzeng T-HK (2016) Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools. PLoS ONE 11(11): e0167100. doi:10.1371/journal.pone.0167100

SAMTOOLS

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics (2009) 25(16) 2078-9 [19505943]

SQUIZZ

ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/

UCSC

https://genome.ucsc.edu/util.html

WIGGLETOOLS

Zerbino DR, Johnson N, Juettemann T, Wilder SP and Flicek PR: WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics 2014 30:1008-1009.