Gap2Seq

Gap2Seq is a program for filling gaps in scaffolds produced by genome assembly tools using short read data such as reads produced by Illumina sequencing.

Publications:

• L. Salmela, K. Sahlin, V. Mäkinen, and A.I. Tomescu: Gap filling as exact path length problem. In Proc. RECOMB 2015, Research in Computational Molecular Biology (ed. T. M. Przytycka), Lecture Notes in Bioinformatics 9029, Springer 2015, 281–292.
  [Article online][Slides presented at RECOMB 2015]
• L. Salmela and A.I. Tomescu: Safely filling gaps with partial solutions common to all solutions. In Proc. WABI '16, Workshop on Algorithms in Bioinformatics (ed. M. Frith and C.N.S. Pedersen), Lecture Notes in Bioinformatics 9838, Springer, 2016, xiv, short abstract.
  [Article online][Slides presented at WABI 2016]
• L. Salmela and A.I. Tomescu: Safely filling gaps with partial solutions common to all solutions. To appear in TCBB.
  [Article online]

A new version of Gap2Seq tailored for insertion genotyping is available in GitHub.

Download:

• Gap2Seq 2.1 source files
• README

Old versions:

• Gap2Seq 2.0 source files
• Gap2Seq 1.0 source files
• Gap2Seq 0.3 source files
• Gap2Seq 0.2 source files
• Gap2Seq 0.1 source files