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alignment
auxiliary
data
preprocessing
simulation
DESCRIPTION.md
README.md

README.md

Finding novel variations of germline immunoglobulin genes using WGS data

This project is dedicated to find new Ig genes from whole genome sequencing data.

Methods

Main method of our investigation is aligning. We try to align reads from WGS data to templates of already known V-genes and find new variants. Now we are using Biopython built-in local aligner which is similar in results to aligner from EMBOSS.

Prerequisites

  1. Mandatory - these are necessary to launch
    • python >= 3.6
    • Biopython >= 1.70
  2. Facultative - using in simulation
    • numpy >= 1.14.0
    • bowtie2 >= 2.2.6
    • samtools >= 1.7
    • bedtools >= 2.25.0

Installing

To copy everything into directory bioinf_vsegments type in shell:

git clone https://github.com/Serfentum/bioinf_vsegments.git

Usage

For now all fuctionality is inside these scripts:

  • align.py - align sequences
  • v_segment_generation.py - generate full V segments
  • read_generation.py - generate reads with noise from sequence

It is subject to change. We are going to make it available for usage from cli, so you shouldn`t try to use until we make everything as it should be.

Version

0.1.0

It is raw version where we are configuring everything on IgH V-segment to make it work properly.

Just wait until release where everything will be done first for IgH V-segment and afterwards for all other chains.

Authors

  • Yana Safonova
  • Andrey Slabodkin
  • Sasha Ilin

References

  1. Greiff, V., Miho, E., Menzel, U., & Reddy, S. T. (2015). Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. Trends in Immunology, 36(11), 738–749. https://doi.org/10.1016/j.it.2015.09.006
  2. Georgiou, G. et. al. (2014). The promise and challenge of high-throughput sequencing of the antibody repertoire, 32(2), 158–168. https://doi.org/10.1038/nbt.2782.The
  3. Yaari, G., & Kleinstein, S. H. (2015). Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Medicine, 7(1), 121. https://doi.org/10.1186/s13073-015-0243-2
  4. Lefranc M-P, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S, Carillon E, Duvergey H, Houles A, Paysan-Lafosse T, Hadi-Saljoqi S, Sasorith S, Lefranc G, Kossida S. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res. 2015 Jan;43(Database issue):D413-22. doi: 10.1093/nar/gku1056. Epub 2014 Nov 5 Free article. PMID: 25378316 LIGM:441
  5. Long, H. X., Li, M. Z., & Fu, H. Y. (2016). Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database. SpringerPlus, 5(1). https://doi.org/10.1186/s40064-016-2526-5
  6. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359
  7. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
  8. Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841–842. https://doi.org/10.1093/bioinformatics/btq033
  9. Lefranc, M. P., Giudicelli, V., Duroux, P., Jabado-Michaloud, J., Folch, G., Aouinti, S., … Kossida, S. (2015). IMGT R, the international ImMunoGeneTics information system R 25 years on. Nucleic Acids Research, 43(D1), D413–D422. https://doi.org/10.1093/nar/gku1056

Acknowledgements

I`d like to thank everybody especially Bioinformatics Institute.

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