SNPidentifier 1.10 – Discover SNPs based on CAP3 Alignments

SNPidentifier 1.10

:: DESCRIPTION

SNPidentifier is designed to predict the location of SNPs from clusters of ESTs produced by the program CAP3. SNPIDENTIFIER is designed for ESTs without accompanying chromatogram sequence quality information, and therefore it performs quality control checks on all data.

::DEVELOPER

NAGRP Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Perl

:: DOWNLOAD

 SNPidentifier

:: MORE INFORMATION

Citation

Gorbach, Danielle M., Zhi-Liang Hu, Zhi-Qiang Du and M. F. Rothschild (2009)
SNP discovery in Litopenaeus vannamei with a new computational pipeline“.
Animal Genetics, 40(1):106-109.

CAP3 / PCAP – Sequence and Genome Assembly Programs

CAP3 / PCAP

:: DESCRIPTION

CAP3 is a sequence assembly program for small-scale assembly of EST sequences with or without quality values.

PCAP is for large-scale assembly of genomic sequences with quality values and with or without forward-reverse read pairs.

::DEVELOPER

Xiaoqiu Huang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 CAP3 / PCAP

:: MORE INFORMATION

Citation:

Huang, X. and Madan, A. (1999)
CAP3: A DNA Sequence Assembly Program.
Genome Research, 9: 868-877.

Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)
PCAP: A Whole-Genome Assembly Program.
Genome Research, 13: 2164-2170.