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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.


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. 
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Meet Marten Boertzer!

Marten is one of the excellent bioinformaticians of BaseClear. He has a lot of experience with analyzing NGS data, and he also developed software such as SSPACE and GapFiller.


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