Citing Bioinformatics Tools and Resources
Common Bioinformatics Tools
| Category | Tool | Citation | DOI |
|---|---|---|---|
| Alignment | Bowtie2 | Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-359. | 10.1038/nmeth.1923 |
| Alignment | STAR | Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. | 10.1093/bioinformatics/bts635 |
| Alignment | BWA | Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-1760. | 10.1093/bioinformatics/btp324 |
| Quality Checks | FastQC | Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Quality Checks | MultiQC | Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047-3048. | 10.1093/bioinformatics/btw354 |
| Read Processing | Trimgalore | ||
| Read Processing | Cutadapt | Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17(1):10-12. | 10.14806/ej.17.1.200 |
| Read Processing | FLASH | Tanja Magoč, Steven L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, Volume 27, Issue 21, November 2011, Pages 2957–2963 | 10.1093/bioinformatics/btr507 |
| Peak Calling | MACS3 | Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. | 10.1186/gb-2008-9-9-r137 |
| Peak Calling | Lanceotron | Lance D Hentges, Martin J Sergeant, Christopher B Cole, Damien J Downes, Jim R Hughes, Stephen Taylor, LanceOtron: a deep learning peak caller for genome sequencing experiments, Bioinformatics, Volume 38, Issue 18, September 2022, Pages 4255–4263 | 10.1093/bioinformatics/btac525 |
| Motif Analysis | MEME Suite | Timothy L. Bailey, Mikael Boden, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, MEME Suite: tools for motif discovery and searching, Nucleic Acids Research, Volume 37, Issue suppl_2, 1 July 2009, Pages W202–W208 | 10.1093/nar/gkp335 |
| Motif Analysis | JASPAR | Baydar Ovek D, Rauluseviciute I, Aronsen DR, Blanc-Mathieu R, Bonthuis I, de Beukelaer H, Ferenc K, Jegou A, Kumar V, Lemma RB, Lucas J, Pochon M, Yun CM, Ramalingam V, Deshpande SS, Patel A, Marinov GK, Wang AT, Aguirre A, Castro-Mondragon JA, Baranasic D, Chèneby J, Gundersen S, Johansen M, Khan A, Kuijjer ML, Hovig E, Lenhard B, Sandelin A, Vandepoele K, Wasserman WW, Parcy F, Kundaje A, Mathelier A JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models Nucleic Acids Res. 2026 Jan 6;54(D1):D184-D193 | 10.1093/nar/gkaf1209 |
| Motif Analysis | Fimo | Charles E. Grant, Timothy L. Bailey, William Stafford Noble, FIMO: scanning for occurrences of a given motif, Bioinformatics, Volume 27, Issue 7, April 2011, Pages 1017–1018 | 10.1093/bioinformatics/btr064 |
| Motif Analysis | HOMER | Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C. Lin, Peter Laslo, Jason X. Cheng, Cornelis Murre, Harinder Singh, Christopher K. Glass,Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities, Molecular Cell, Volume 38, Issue 4,2010,Pages 576-589, ISSN 1097-2765 | 10.1016/j.molcel.2010.05.004 |
| Visualization | deepTools | Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, Thomas Manke, deepTools: a flexible platform for exploring deep-sequencing data, Nucleic Acids Research, Volume 42, Issue W1, 1 July 2014, Pages W187–W191 | 10.1093/nar/gku365 |
| Visualization | IGV | Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24-26. | 10.1038/nbt.1754 |
| R Package | DESeq2 | Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014) | 10.1186/s13059-014-0550-8 |
| R Package | ChIPseeker | Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31(14):2382-2383. | 10.1093/bioinformatics/btv145 |
| R Package | plotgardener | Nicole E Kramer, Eric S Davis, Craig D Wenger, Erika M Deoudes, Sarah M Parker, Michael I Love, Douglas H Phanstiel, Plotgardener: cultivating precise multi-panel figures in R, Bioinformatics, Volume 38, Issue 7, March 2022, Pages 2042–2045 | 10.1093/bioinformatics/btac057 |
Other tools and softwares
| Category | Tool | Citation | DOI |
|---|---|---|---|
| HiC Analysis | HiC-Pro | Servant, N., Varoquaux, N., Lajoie, B.R. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16, 259 (2015) | 10.1186/s13059-015-0831-x |
| HiC Analysis | ICE | Imakaev, M., Fudenberg, G., McCord, R. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9, 999–1003 (2012) | 10.1038/nmeth.2148 |
| Capture-C Analysis | Capture-C Tools | Davies, J., Telenius, J., McGowan, S. et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 13, 74–80 (2016) | 10.1038/nmeth.3664 |
| Capture-C Analysis | CHiCAGO | Cairns, J., Freire-Pritchett, P., Wingett, S. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol 17, 127 (2016) | 10.1186/s13059-016-0992-2 |
Example Methods Section
Here’s an example of how to incorporate citations in a methods section:
Raw sequencing reads were quality-checked using FastQC (Andrews, 2010) and trimmed with Trimmomatic (Bolger et al., 2014). Reads were aligned to the mm10 reference genome using Bowtie2 version 2.4.5 (Langmead & Salzberg, 2012). Peak calling was performed using MACS2 version 2.2.7 (Zhang et al., 2008) with default parameters. Visualization tracks were generated using deepTools bamCoverage (Ramírez et al., 2016) and viewed in the UCSC Genome Browser (Kent et al., 2002).
Best Practices
- Version control: Always note the version of software used
- Parameters: Document non-default parameters in your methods
- Scripts: Share analysis scripts in repositories like GitHub
- Docker/Conda: Consider using containers for complete reproducibility
- RRID: Use Research Resource Identifiers (RRIDs) when available