References

Software Packages in BD Rhapsody™ Sequence Analysis Pipeline

anndata

Isaac Virshup et al. (2021). anndata: Annotated data. bioRxiv. doi: 10.1101/2021.12.16.473007.

Cock et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, Volume 25, Issue 11, June 2009, Pages 1422–1423, https://doi.org/10.1093/bioinformatics/btp163

bowtie2

bowtie2: Fast and sensitive read alignment. [Software]. https://bowtie-bio.sourceforge.net/bowtie2/index.shtml

bwa-mem2

Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. 10.1109/IPDPS.2019.00041

cython

Behnel, S., Bradshaw, R., Citro, C., Dalcin, L., Seljebotn, D. S., & Smith, K. (2011). Cython: The best of both worlds. Computing in Science & Engineering, 13(2), 31–39. https://ieeexplore.ieee.org/document/5582062

htseq

Putri et al. (2022). Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166. https://doi.org/10.1093/bioinformatics/btac166

IGBlast

Ye, J., Ma, N., Madden, T. L., & Ostell, J. M. (2013). IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic acids research, 41(Web Server issue), W34–W40. https://doi.org/10.1093/nar/gkt382

jinja2

Pallets Projects. (2023). Jinja2. [Software]. https://palletsprojects.com/p/jinja/

matplotlib

J. D. Hunter. (2007). Matplotlib: A 2D Graphics Environment, Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95. https://ieeexplore.ieee.org/document/4160265

muon

Bredikhin, D., Kats, I. & Stegle, O. (2022). MUON: multimodal omics analysis framework. Genome Biology 2022 Feb 01. doi: 10.1186/s13059-021-02577-8.

numba

Lam, S. K., Pitrou, A., & Seibert, S. (2015). Numba: A llvm-based python jit compiler. In Proceedings of the Second Workshop on the LLVM Compiler Infrastructure in HPC (pp. 1–6). https://numba.pydata.org/

numpy

Harris, C.R., Millman, K.J., van der Walt, S.J. et al. (2020).Array programming with NumPy. Nature 585, 357–362 (2020). https://doi.org/10.1038/s41586-020-2649-2

opentsne

Pavlin G. Poličar, Martin Stražar and Blaž Zupan. (2019). openTSNE: a modular Python library for t-SNE dimensionality reduction and embedding. bioRxiv. https://www.biorxiv.org/content/10.1101/731877v3

pandas

pandas development team. (2021). pandas-dev/pandas: Pandas (v2.1.0rc0). Zenodo. https://doi.org/10.5281/zenodo.605272

pigz

The pigz developement team. (2023). pigz: A parallel implementation of gzip for modern multi-processor, multi-core machines. [Software]. https://zlib.net/pigz/

pyir

Soto, C. et al. (2020). PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. BMC Bioinformatics. https://github.com/crowelab/PyIR

pysam

pysam: a Python module for reading and manipulating SAM/BAM files. [Software]. https://github.com/pysam-developers/pysam

python-levenshtein

Max Bachmann. (2022). python-levenshtein. [Software]. https://github.com/maxbachmann/python-Levenshtein

scikit-learn

Pedregosa et al. (2011). Scikit-learn: Machine Learning in Python, JMLR 12, pp. 2825-2830, 2011. https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html

scipy

Virtanen et.al. (2020) SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods, 17(3), 261-272. https://www.nature.com/articles/s41592-019-0686-2

seaborn

Waskom, M. L., (2021). seaborn: statistical data visualization. Journal of Open Source Software, 6(60), 3021, https://doi.org/10.21105/joss.03021

seqtk

Li, H. et al. (2023). Seqtk: a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. [Software]. https://github.com/lh3/seqtk

seurat

Hao, Y. et al. (2021). “Integrated analysis of multimodal single-cell data.” Cell. doi:10.1016/j.cell.2021.04.048, https://doi.org/10.1016/j.cell.2021.04.048.

signac

Stuart, T. et al. (2021). "Single-cell chromatin state analysis with Signac." Nature Methods. doi:10.1038/s41592-021-01282-5, https://doi.org/10.1038/s41592-021-01282-5

sinto

sinto: single-cell analysis tools. [Software]. https://github.com/timoast/sinto

STAR

Dobin, A. et al. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England), 29(1), 15–21. https://doi.org/10.1093/bioinformatics/bts635

tensorflow-cpu

Martin et al. (2016). TensorFlow: A system for large-scale machine learning. In Proceedings of the 12th USENIX Symposium on Operating Systems Design and Implementation. 265–283.https://dl.acm.org/doi/10.5555/3026877.3026899

Trinity

Grabherr, M. et al. (2011). Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52.

BD Rhapsody™ Sequence Analysis Pipeline 2.2.1