GapFiller

GapFiller is a seed-and-extend local assembler to fill the gap within paired reads.
It can be used for both DNA and RNA and it has been tested on Illumina data.
GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length.

Features

Supported input format: FASTQ (.gz, .bz2), FASTA (.gz, .bz2), SAM, BAM
Highly customizable assembly parameters
Possibility to specify different datasets for seeding and assembly
Possibility to store layout information (read position and orientation within assembled contigs)

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