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2 user reviews
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Hello. We have 250x2 PE reads of the insert size ~400bp, and also mate pair libraries of 3kb, 7kb and 10kb inserts. Is it possible to use all of these reads jointly for detecting variations? I am mainly using this to perform a final polishing of our de novo genome assembly (from the same data).
No open topic.
- Software type:
- Restrictions to use:
- Programming languages:
- Perl, Python, Shell (Bash)
- Computer skills:
- Dbfasta, BWA, Picard, Samtools, BioPerl, Bedtools
- Command line interface
- Operating system:
- GNU General Public License version 3.0
- Source code URL:
- Caleb Davis <caldavis at gmail.com>
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- (Davis CF et al., 2016) SV-STAT accurately detects structural variation via alignment to reference-based assemblies. Source Code Biol Med. PMID: 27330550 DOI: 10.1186/s13029-016-0051-0
Structural and Computational Biology and Molecular Biophysics (SCBMB) Program, Baylor College of Medicine, Houston, TX, USA; Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA; W. M. Keck Center for Interdisciplinary Bioscience Training, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
This work was supported by the following grants from the NIH: National Institute of General Medical Sciences (K12 GM084897), and a training fellowship from the Keck Center for Interdisciplinary Bioscience Training of the Gulf Coast Consortia (T15 LM007093).