barcode toolkit

Tools to automate processing of barcode sequences, design and test barcoding primers

Installation

This toolkit is for unix based system only (e.g. Linux, MAC or WSL)

In the terminal, type the following command in the desired installation directory:

git clone https://github.com/lentendu/barcode_toolkit.git

You can add the bin directory into your PATH variable to access the executables from everywere on your system, using, for example, the following line:

echo "PATH=\$PATH:$PWD/barcode_toolkit/bin" >> ~/.bashrc

Dependencies

• BLAST+ v2.10+ (Camacho et al., 2009)
• barrnap (Seemann, 2024) for nanobass
• biom-format (McDonald et al., 2012) for probe_sra_marker
• canu (Koren et al., 2017) for nanobass
• cutadapt v3+ (Martin, 2011)
• Entrez Direct (EDirect) (Kans, 2023)
• GNU parallel
• goalign v0.3.4+ (Lemoine & Gascuel, 2021)
• IBM Aspera Connect for probe_sra_marker
• HMMER v3+ (Eddy, 2011)
• mafft v7.487+ (Katoh & Standley, 2013)
• NGmerge v0.3+ (Gaspar, 2018)
• PANDAseq v2.10+ (Masella et al., 2012) for probe_sra_marker
• pv
• RATTLE (de la Rubia et al., 2022) for nanobass
• SeqKit v0.15.0+ (Shen et al., 2016)
• swarm v2+ (Mahé et al., 2015)
• taxonkit v0.11.0+ (Shen & Ren, 2021)
• tracy v0.7+ (Rausch et al.,2020)
• vsearch v2+ (Rognes et al., 2016) for probe_sra_marker

Usage

apolla is a tool to search for a probe specific to a target clade.

consensus_blast is a tool for automatic BLAST of multiple sequences and creating a consensus taxonomy from a range of best matches.

nanobass is a tool to assemble barcoding Nanopore sequences.

primcheck is a tool to perform in-silico PCR and evaluate primer pairs performance to amplify a target clade.

primdesign is a tool to automatically design primer pairs for target clade PCR amplification.

probe_sra_marker is a tool to extract reads matching a probe from short reads archive marker gene run files.

sanger_cleaner is a tool for basecalling and quality trimming of Sanger sequences using tracy, sickle, cutadapt, mafft and goalign.

Any of these tools can be call with the -h option to see full options and usage.

References

• Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421. 10.1186/1471-2105-10-421
• Eddy, S. R. (2011). Accelerated Profile HMM Searches. PLOS Computational Biology, 7(10), e1002195. 10.1371/journal.pcbi.1002195
• Gaspar, J. M. (2018). NGmerge: Merging paired-end reads via novel empirically-derived models of sequencing errors. BMC Bioinformatics, 19(1), 536. doi:10.1186/s12859-018-2579-2
• Kans, J. (2023). Entrez Direct: E-utilities on the Unix Command Line. In Entrez Programming Utilities Help [Internet]. National Center for Biotechnology Information (US). https://www.ncbi.nlm.nih.gov/books/NBK179288/
• Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. doi:10.1093/molbev/mst010
• Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, 27(5), 722–736. 10.1101/gr.215087.116
• Lemoine, F., & Gascuel, O. (2021). Gotree/Goalign: Toolkit and Go API to facilitate the development of phylogenetic workflows. NAR Genomics and Bioinformatics, 3(3), doi:10.1093/nargab/lqab075
• Mahé, F., Rognes, T., Quince, C., de Vargas, C., Dunthorn, M., 2015. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 3, e1420. doi:10.7717/peerj.1420
• Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal, 17(1), 10–12. doi:10.14806/ej.17.1.200
• Masella, A.P., Bartram, A.K., Truszkowski, J.M., Brown, D.G., Neufeld, J.D., 2012. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13, 31. doi:10.1186/1471-2105-13-31
• McDonald, D., Clemente, J.C., Kuczynski, J., Rideout, J.R., Stombaugh, J., Wendel, D., Wilke, A., Huse, S., Hufnagle, J., Meyer, F., Knight, R., Caporaso, J.G., 2012. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience 1. doi:10.1186/2047-217X-1-7
• Rausch, T., Fritz, M. H.-Y., Untergasser, A., & Benes, V. (2020). Tracy: Basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files. BMC Genomics, 21(1), 230. doi:10.1186/s12864-020-6635-8
• Rognes, T., Flouri, T., Nichols, B., Quince, C., Mahé, F., 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ. doi:10.7717/peerj.2584
• de la Rubia, I., Srivastava, A., Xue, W., Indi, J. A., Carbonell-Sala, S., Lagarde, J., Albà, M. M., & Eyras, E. (2022). RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing. Genome Biology, 23(1), 153. 10.1186/s13059-022-02715-w
• Seemann, T. (2024). BAsic Rapid Ribosomal RNA Predictor [Perl] barrnap (Original work published 2013)
• Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE, 11(10), e0163962. doi:10.1371/journal.pone.0163962
• Shen, W., & Ren, H. (2021). TaxonKit: A practical and efficient NCBI taxonomy toolkit. Journal of Genetics and Genomics, 48(9), 844–850. doi:10.1016/j.jgg.2021.03.006