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  3. Genome annotation
  4. Repetitive DNA
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It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Programming languages:
C, C++, Java
Computer skills:
Advanced
Stability:
Stable
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  • (Mose et al., 2014) ABRA: improved coding indel detection via assembly based re-alignment. Bioinformatics.
    PMID: 24907369
  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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