Next Generation Sequencing: Inventory

From BioAssist
Jump to: navigation, search

Return to the main page of Next Generation Sequencing

Sequencing Machines

Group Illumina GAII Illumina HiSeq2000 454 SOLiD Others
Wageningen University, Bioinformatics group 1
Leiden University Medical Center, Center for Human and Clinical Genetics 2 1 1 1 Helicos
Amsterdam Medical Center, Clinical Epidemiology 1 1
Erasmus Medical Center, Biomics group 1 1
Erasmus Medical Center, Complex Genetics group 2
University Medical Center Groningen, Genomics Coordination Centre 1 1
Hubrecht Institute, Genome Biology group 1 2
Nijmegen Centre for Molecular Life Sciences, Department of Human Genetics 1 3

Or view it from a Google Map

Quality Control

Tools
Group Illumina pipeline 454 pipeline Customized scripts Helicos pipeline SOLiD pipeline FastQC
Wageningen University, Bioinformatics group x x x
Leiden University Medical Center, Center for Human and Clinical Genetics x x GAPSS x
Amsterdam Medical Center x customized adaptors x x
Erasmus Medical Center, Biomics group x Allele specific counting & iSeq
University Medical Center Groningen, Genomics Coordination Centre x x
Hubrecht Institute, Genome Biology group x
Radboud University Nijmegen Medical Center, Genomic Disorders group x x x

De Novo Assembly

Tools
Group Newbler SOAPdenovo Cabog Velvet ClC Bio AbYSS
Wageningen University, Bioinformatics group x x x x x x
Amsterdam Medical Center, Clinical Epidemiology x x
Erasmus Medical Center, Biomics group x x
Leiden University Medical Center, Center for Human and Clinical Genetics x
Hubrecht Institute, Genome Biology group

Mapping Alignment

Tools
Group Wageningen University, Bioinformatics group Amsterdam Medical Center, Clinical Epidemiology Erasmus Medical Center, Biomics group Leiden University Medical Center, Center for Human and Clinical Genetics Hubrecht Institute, Genome Biology group University Medical Center Groningen, Genomics Coordination Centre Radboud University Nijmegen Medical Center
Bowtie x x x x
BWA x x x x
CASAVA x x
454 mapper x x x x
ClC Bio x x x x
Eland x x
SOAP x
Mapread (cs)? x x
BLAT x x
BLAST x x
Helisphere x
Stampy x

Reporting

Tools
Group Wageningen University, Bioinformatics group Amsterdam Medical Center, Clinical Epidemiology Erasmus Medical Center, Biomics group Leiden University Medical Center, Center for Human and Clinical Genetics Hubrecht Institute, Genome Biology group University Medical Center Groningen, Genomics Coordination Centre Radboud University Nijmegen Medical Center
CLC Bio x x
SAM Tools (Galaxy) x x x
GGB x
Customized scripts x x x x x
R scripts x x x x
UCSC Browser x x x x
Spreadsheet (Excel/OpenOffice) x x
GNU plot x