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)

Project Activity

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Categories

Bio-Informatics

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Additional Project Details

Operating Systems

Linux

User Interface

Command-line

Programming Language

C++

Related Categories

C++ Bio-Informatics Software

Registered

2012-08-10