GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. It is unique in offering the possibility to manually control the gap closure process. By using the distance information of paired-read data, GapFiller seeks to close the gap from each edge in an iterative manner. From a good number of tests we see the program yields excellent results both on bacterial en eukaryotic  data sets. The command-line Perl script and additional files can be downloaded below. The input data is given by pre-assembled scaffold sequences (FASTA) and NGS paired-read data (FASTA or FASTQ). The final gap-filled scaffolds are provided in FASTA format. GapFiller has been published in Genome Biology (2012, 13(6):56).

Obtaining GapFiller

In principal the basic version of GapFiller is free for academics, upgrades are available against a small additional fee. Commercial users need in any case to pay for a license, the exact fee depends on the size of the institution (number of employees) and the type of usage (R&D or commercial services). If you are interested in a copy of our software, please fill in your contact details below. Note that our software is distributed on a weekly basis. For more information about licenses and premium packages please contact us at

Meet Walter Pirovano!

Walter Pirovano (PhD) is the Director of the Product Development department and a member of the BaseClear Management Team. He supervises our team of excellent product managers with expertise in the field of microbiome analysis, microbial genomics, regulatory affairs, bioinformatics and (far) beyond.

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