PALEOMIX 1.2.5 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

PALEOMIX 1.2.5

:: DESCRIPTION

The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.

::DEVELOPER

The Orlando Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PALEOMIX

:: MORE INFORMATION

Citation

Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10.
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Schubert M1, Ermini L1, Der Sarkissian C1, Jónsson H1, Ginolhac A1, Schaefer R2, Martin MD1, Fernández R1, Kircher M3, McCue M4, Willerslev E1, Orlando L1.

GeMS 1.0 – A High Efficient SNP Detection Software

GeMS 1.0

:: DESCRIPTION

GeMS (Genotype Model Selection) is a single nucleotide polymorphism (SNP) detector that works with alignment files of high-throughput sequencing (HTS) data. GeMS calls SNPs based on a statistical model selection procedure and accounts for the aerrors that can occur during genomic sample preparation

::DEVELOPER

Cui Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 GeMS

:: MORE INFORMATION

Citation

Na You, Gabriel Murillo, Kang Ning, Xiaoquan Su, Xiaowei Zheng, Jian Xu, Shoudong Zhang, Jiankang Zhu and Xinping Cui.
SNP calling using genotype model selection on next generation sequencing data“,
Bioinformatics. 2012 Mar 1;28(5):643-50. doi: 10.1093/bioinformatics/bts001.

linkSNPs 1.0 beta – SNP Detection and Haplotype Reconstruction

linkSNPs 1.0 beta

:: DESCRIPTION

linkSNPs is a SNP detection tool with haplotype information from an individual sample.

::DEVELOPER

the INNAN Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Perl

:: DOWNLOAD

 linkSNPs

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Jun 28. [Epub ahead of print]
The Linkage Method: A Novel Approach for SNP Detection and Haplotype Reconstruction from a Single Diploid Individual Using Next-Generation Sequence Data.
Sasaki E, Sugino RP, Innan H.