BaseClear offers a wide range of bioinformatics solutions, primarily in the area of Next Generation Sequencing (NGS) data analysis. For this we mainly make a choice out of the most advanced software packages available on the market. However, especially in such a dynamic field as NGS, we frequently develop our own software solutions to fill in the gaps that are not covered by existing tools. Some of our analysis setups are published in collaboration with other groups, in some cases we decide to share stand-alone tools with the scientific community. At present our bioinformatics team has published a number of high-impact papers which underscores the scientific excellence of our team. We see our tools and pipelines as important features that are part of our complete solutions packages. In this manner we can guarantees our customers to receive outstanding results that fully answer their research questions.

BaseTools software

  • SSPACE-standard
    • Stand-alone program for scaffolding pre-assembled contigs
    • Uses the distance information of paired-end and/or mate-pair data to assess the order, distance and orientation of contigs
    • Input data: pre-assembled contig sequences (FASTA) and NGS paired-read data (FASTA or FASTQ)
    • Final scaffolds are provided in FASTA format.
    • Manually control the scaffolding process
  • SSPACE-LongRead
    • Stand-alone program for scaffolding pre-assembled contigs
    • Uses the long read information to place contigs or scaffold in the right order and orientation into super-scaffolds
    • Input data: long reads data (e.g. PacBio sequencing reads)
  • GapFiller
    • Stand-alone program for closing gaps within pre-assembled scaffolds
    • Uses the distance information of paired-read data to close the gap from each edge in an iterative manner
    • Input data: pre-assembled scaffold sequences (FASTA) and NGS paired-read data (FASTA or FASTQ)
    • Final gap-filled scaffolds are provided in FASTA format
    • Manually control the gap closure process


  • SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. Boetzer M, Pirovano W. BMC Bioinformatics. 2014 Jun 20;15:211. doi: 10.1186/1471-2105-15-211.
  • The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK. Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6. doi: 10.1073/pnas.1314702110.
  • SNP genotyping for detecting the ‘rare allele phenomenon’ in hybrid zones. Lammers Y, Kremer D, Brakefield PM, Groenenberg DS, Pirovano W, Schilthuizen M. Mol Ecol Resour. 2013 Mar;13(2):237-42. doi: 10.1111/1755-0998.12044.
  • First draft genome sequence of the Japanese eel, Anguilla japonica. Henkel CV, Dirks RP, de Wijze DL, Minegishi Y, Aoyama J, Jansen HJ, Turner B, Knudsen B, Bundgaard M, Hvam KL, Boetzer M, Pirovano W, Weltzien FA, Dufour S, Tsukamoto K, Spaink HP, van den Thillart GE. Gene. 2012 Dec 15;511(2):195-201. doi: 10.1016/j.gene.2012.09.064.
  • Towards almost closed genomes with GapFiller. Boetzer M, Pirovano W. Genome Biol. 2012 Jun 25;13(6):R56. doi: 10.1186/gb-2012-13-6-r56.
  • Scaffolding pre-assembled contigs using SSPACE. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Bioinformatics. 2011 Feb 15;27(4):578-9. doi: 10.1093/bioinformatics/btq683.

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