Verktøykasse

Containerized bioinformatic tools

• BreakDancer

Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., Shi, X., Fulton, R. S., Ley, T. J., Wilson, R. K., Ding, L., & Mardis, E. R. (2009). BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nature Methods, 6(9), 677–681.

• BamTools

https://github.com/pezmaster31/bamtools

• bamUtil

Jun, G., Wing, M. K., Abecasis, G. R., & Kang, H. M. (2015). An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Research, 25(6), 918–925.

• bwa

Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754–1760.

• bwa-mem2

Md, V., Misra, S., Li, H., & Aluru, S. (2019). Efficient architecture-aware acceleration of BWA-MEM for multicore systems. Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium, IPDPS 2019, 314–324.

• CNVkit

Talevich, E., Shain, A. H., Botton, T., & Bastian, B. C. (2016). CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Computational Biology, 12(4), 1–18.

• CNVnator

Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011). CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research, 21(6), 974–984.

• CoNIFER

Krumm, N., Sudmant, P. H., Ko, A., O’Roak, B. J., Malig, M., Coe, B. P., Quinlan, A. R., Nickerson, D. A., & Eichler, E. E. (2012). Copy number variation detection and genotyping from exome sequence data. Genome Research, 22(8), 1525–1532.

• cutadapt

Martin, M. (2010). Cutadapt removes adapter sequences from high-throughput sequencing reads. Technical Notes, 17(1), 10–12.

• DELLY2

Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Benes, V., & Korbel, J. O. (2012). DELLY: Structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics, 28(18), 333–339.

• fastp

Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890.

• FastQ Screen

Wingett, S. W., & Andrews, S. (2018). Fastq screen: A tool for multi-genome mapping and quality control. F1000Research, 7(0), 1–13.

• FastQC

Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data.

• InDelible

Gardner, E. J., Sifrim, A., Lindsay, S. J., Prigmore, E., Rajan, D., Danecek, P., Gallone, G., Eberhardt, R. Y., Martin, H. C., Wright, C. F., Fitzpatrick, D. R., Firth, H. V, & Hurles, M. E. (2020). InDelible: Detection and Evaluation of Clinically-relevant Structural Variation from Exome Sequencing. MedRxiv.

• InterOp

Illumina

• LUMPY

Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014). LUMPY: A probabilistic framework for structural variant discovery. Genome Biology, 15(6), 1–19.

• Manta

Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Cox, A. J., Kruglyak, S., & Saunders, C. T. (2016). Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32(8), 1220–1222.

• mosdepth

Pedersen, B. S., & Quinlan, A. R. (2018). Mosdepth: Quick coverage calculation for genomes and exomes. Bioinformatics, 34(5), 867–868.

• MultiQC

Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048.

• ONCOCNV

Boeva, V., Popova, T., Lienard, M., Toffoli, S., Kamal, M., Le Tourneau, C., ... & Laes, J. F. (2014). Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. Bioinformatics, 30(24), 3443-3450.

• Pindel

Ye, K., Schulz, M. H., Long, Q., Apweiler, R., & Ning, Z. (2009). Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25(21), 2865–2871.

• QUAST

Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075.

• R

R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

• seqtools

https://github.com/seandavi/SDST

• simple_sv_annotation

https://github.com/AstraZeneca-NGS/simple_sv_annotation

• SnpEff

Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, 6(2), 80–92.

• SortMeRNA

Kopylova, E., Noé, L., & Touzet, H. (2012). SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics, 28(24), 3211–3217.

• SPAdes

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455–477.

• STAR

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15–21.

• Strelka

Kim, S., Scheffler, K., Halpern, A. L., Bekritsky, M. A., Noh, E., Källberg, M., Chen, X., Kim, Y., Beyter, D., Krusche, P., & Saunders, C. T. (2018). Strelka2: fast and accurate calling of germline and somatic variants. Nature Methods, 15(8), 591–594.

• TIDDIT

Eisfeldt, J., Vezzi, F., Olason, P., Nilsson, D., & Lindstrand, A. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research, 6(0), 664.

• Trimmomatic

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120.

• Unicycler

Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Computational Biology, 13(6), 1–22.

• VarDict

Lai, Z., Markovets, A., Ahdesmaki, M., Chapman, B., Hofmann, O., Mcewen, R., Johnson, J., Dougherty, B., Barrett, J. C., & Dry, J. R. (2016). VarDict: A novel and versatile variant caller for next-generation sequencing in cancer research. Nucleic Acids Research, 44(11), 1–11.

• VCFtools

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., & Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158.

• VEP

McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016). The Ensembl Variant Effect Predictor. Genome Biology, 17(1), 1–14.