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references.md 3.92 KiB

References

  1. python:
  1. trimgalore:
  1. cutadapt:
  • Marcel, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1):10-12. doi:10.14806/ej.17.1.200
  1. bwa:
  • Li H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25: 1754-60. doi:10.1093/bioinformatics/btp324
  1. samtools:
  • Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:10.1093/bioinformatics/btp352
  1. sambamba:
  • Tarasov, A., A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. 2015 Sambamba: fast processing of NGS alignment formats. Bioinformatics 31(12): 2032-2034. doi:10.1093/bioinformatics/btv098
  1. bedtools:
  • Quinlan, A. R., and I. M. Hall. 2010. BEDTools: a flexible suite of utilities for comparing genomic feautures. Bioinformatics 26(6): 841-842. doi:10.1093/bioinformatics/btq033
  1. deeptools:
  • Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:10.1093/nar/gkw257
  1. phantompeakqualtools:
  • Landt S. G., G. K. Marinov, A. Kundaje, et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 9: 1813-31. doi:10.1101/gr.136184.111
  • Kharchenko P. K., M. Y. Tolstorukov, and P. J. Park. 2008. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26(12): 1351-1359. doi:10.1038/nbt.1508
  1. macs:
  • Zhang Y., T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson, B. E. Bernstein, C. Nusbaum, R. M. Myers, M. Brown, W. Li, and X. S. Liu. 2008. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137. doi:10.1186/gb-2008-9-9-r137
  1. UCSC(bedGraphToBigWig):
  • Kent W. J., A. S. Zweig, G. Barber, A. S. Hinrichs, and D. Karolchik. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics 26(17): 2204-2207. doi:10.1093/bioinformatics/btq351
  1. R:
  • R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL:http://www.R-project.org/.
  1. MultiQc:
  • Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:10.1093/bioinformatics/btw354
  1. BICF ChIP-seq Analysis Workflow:
  • Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.0). Zenodo. doi:10.5281/zenodo.3891417
  1. Nextflow: