SeCaPr v1.1.15 – SEquence CApture PRocessor

SeCaPr v1.1.15

:: DESCRIPTION

SeCaPr is a computational pipeline for processing Illumina sequence capture data

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python

:: DOWNLOAD

SeCaPr

:: MORE INFORMATION

Citation

PeerJ. 2018 Jul 13;6:e5175. doi: 10.7717/peerj.5175. eCollection 2018.
SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments.
Andermann T, Cano á, Zizka A, Bacon C, Antonelli A

3PD – Primer design for Chromosome Conformation Capture Assays

3PD

:: DESCRIPTION

3PD is a bioinformatics solution  to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays.

::DEVELOPER

3PD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 29;10:635. doi: 10.1186/1471-2164-10-635.
3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Fröhler S, Dieterich C.

METCAP – Probe Generation Tool for Large-scale Targeted Metagenomics Sequence Capture

METCAP

:: DESCRIPTION

MetCap is a web-based tool that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies.

::DEVELOPER

MetCap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.
Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D.
BMC Bioinformatics. 2015 Feb 28;16(1):65.

Wessim 1.0 – Whole Exome Sequencing SIMulator using in silico exome capture

Wessim 1.0

:: DESCRIPTION

Wessim is a simulator for a targeted resequencing as generally known as exome sequencing. Wessim basically generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.

::DEVELOPER

Sangwoo Kim

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

  Wessim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1076-7. doi: 10.1093/bioinformatics/btt074. Epub 2013 Feb 14.
Wessim: a whole-exome sequencing simulator based on in silico exome capture.
Kim S, Jeong K, Bafna V.