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.
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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