Table 1 Assemblathon 2 participating team details
From: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Team name | Team identifier | Number of assemblies submitted | Sequence data used for bird assembly | Institutional affiliations | Principal assembly software used | ||
|---|---|---|---|---|---|---|---|
| Â | Â | Bird | Fish | Snake | Â | Â | Â |
ABL | ABL | 1 | 0 | 0 | 4 + I | Wayne State University | HyDA |
ABySS | ABYSS | 0 | 1 | 1 | Â | Genome Sciences Centre, British Columbia Cancer Agency | ABySS and Anchor |
Allpaths | ALLP | 1 | 1 | 0 | I | Broad Institute | ALLPATHS-LG |
BCM-HGSC | BCM | 2 | 1 | 1 | 4 + I + P1 | Baylor College of Medicine Human Genome Sequencing Center | SeqPrep, KmerFreq, Quake, BWA, Newbler, ALLPATHS-LG, Atlas-Link, Atlas-GapFill, Phrap, CrossMatch, Velvet, BLAST, and BLASR |
CBCB | CBCB | 1 | 0 | 0 | 4 + I + P | University of Maryland, National Biodefense Analysis and Countermeasures Center | Celera assembler and PacBio Corrected Reads (PBcR) |
CoBiG2 | COBIG | 1 | 0 | 0 | 4 | University of Lisbon | 4Pipe4 pipeline, Seqclean, Mira, Bambus2 |
CRACS | CRACS | 0 | 0 | 1 | Â | Institute for Systems and Computer Engineering of Porto TEC, European Bioinformatics Institute | ABySS, SSPACE, Bowtie, and FASTX |
CSHL | CSHL | 0 | 3 | 0 | Â | Cold Spring Harbor Laboratory, Yale University, University of Notre Dame | Metassembler, ALLPATHS, SOAPdenovo |
CTD | CTD | 0 | 3 | 0 | Â | National Research University of Information Technologies, Mechanics, and Optics | Unspecified |
Curtain | CURT | 0 | 0 | 1 | Â | European Bioinformatics Institute | SOAPdenovo, fastx_toolkit, bwa, samtools, velvet, and curtain |
GAM | GAM | 0 | 0 | 1 | Â | Institute of Applied Genomics, University of Udine, KTH Royal Institute of Technology | GAM, CLC and ABySS |
IOBUGA | IOB | 0 | 2 | 0 | Â | University of Georgia, Institute of Aging Research | ALLPATHS-LG and SOAPdenovo |
MLK Group | MLK | 1 | 0 | 0 | I | UC Berkeley | ABySS |
Meraculous | MERAC | 1 | 1 | 1 | I | DOE Joint Genome Institute, UC Berkeley | meraculous |
Newbler-454 | NEWB | 1 | 0 | 0 | 4 | 454 Life Sciences | Newbler |
Phusion | PHUS | 1 | 0 | 1 | I | Wellcome Trust Sanger Institute | Phusion2, SOAPdenovo, SSPACE |
PRICE | PRICE | 0 | 0 | 1 | Â | UC San Francisco | PRICE |
Ray | RAY | 1 | 1 | 1 | I | CHUQ Research Center, Laval University | Ray |
SGA | SGA | 1 | 1 | 1 | I | Wellcome Trust Sanger Institute | SGA |
SOAPdenovo | SOAP | 3 | 1 | 1 | I2 | BGI-Shenzhen, HKU-BGI | SOAPdenovo |
Symbiose | SYMB | 0 | 1 | 1 | Â | ENS Cachan/IRISA, INRIA, CNRS/Symbiose | Monument, SSPACE, SuperScaffolder, and GapCloser |