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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
   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
  1. 1BCM-HGSC team also included an evaluation bird assembly with Illumina and Roche 454 data only.
  2. 2One of the two evaluation assemblies by the SOAPdenovo team included a bird assembly that used Roche 454 and Illumina.
  3. 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.