Table 1.
Assemblathon 2 participating team details
| Team name | Team identifier | Number of assemblies submitted | Sequence data used for bird assembly | Institutional affiliations | Principal assembly software used | ||
|---|---|---|---|---|---|---|---|
| |
|
Bird |
Fish |
Snake |
|
|
|
| ABL |
ABL |
1 |
0 |
0 |
4 + I |
Wayne State University |
HyDA |
| ABySS |
ABYSS |
0 |
1 |
1 |
|
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 |
|
Institute for Systems and Computer Engineering of Porto TEC, European Bioinformatics Institute |
ABySS, SSPACE, Bowtie, and FASTX |
| CSHL |
CSHL |
0 |
3 |
0 |
|
Cold Spring Harbor Laboratory, Yale University, University of Notre Dame |
Metassembler, ALLPATHS, SOAPdenovo |
| CTD |
CTD |
0 |
3 |
0 |
|
National Research University of Information Technologies, Mechanics, and Optics |
Unspecified |
| Curtain |
CURT |
0 |
0 |
1 |
|
European Bioinformatics Institute |
SOAPdenovo, fastx_toolkit, bwa, samtools, velvet, and curtain |
| GAM |
GAM |
0 |
0 |
1 |
|
Institute of Applied Genomics, University of Udine, KTH Royal Institute of Technology |
GAM, CLC and ABySS |
| IOBUGA |
IOB |
0 |
2 |
0 |
|
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 |
|
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 | ENS Cachan/IRISA, INRIA, CNRS/Symbiose | Monument, SSPACE, SuperScaffolder, and GapCloser | |
1BCM-HGSC team also included an evaluation bird assembly with Illumina and Roche 454 data only.
2One of the two evaluation assemblies by the SOAPdenovo team included a bird assembly that used Roche 454 and Illumina.
Team identifiers are used to refer to assemblies in figures (Additional file 2: Table S1 lists alternative identifiers used during the evaluation phase). Sequence data types for bird assemblies are: Roche 454 (4), Illumina (I), and Pacific Biosciences (P). Additional details of assembly software, including version numbers and CPU/RAM requirements of software are provided in Additional file 2: Tables S2 and S3. Detailed assembly instructions are available for some assemblies in Additional file 3.