RACA: Reference-Assisted Chromosome Assembly

• RACA source v1.0 (Used in the PNAS paper)
• RACA source v1.1 (With some additional error handling)
• 04/17/2014 - A minor bug fixed. Thanks Huifen (Beijing Normal University, China)
• 07/16/2014 - Additional error handling in the script/estparJK.pl file. Thanks Mikhail Kolmogorov (St. Petersburg University, Russia)
• Tibetan antelope (TA) data (3.8 GB) that includes the followings:
• TA scaffold sequences
• TA read mapping results by the SOAP2 program
• Chains and Nets by mapping TA and human(hg18) to cattle(umd3)
• And all required parameter files for running RACA
• 04/04/2014 - Description in the "insertsize_sd.txt" file has been corrected. Thanks Manhui Wang (Cardiff University, UK)
• Simulated genome sequences (153 MB)
• Simulated genome sequence fragments (586 MB)
• Chains and Nets of simulated genome sequences (159 MB)
• Evaluation results by using the GAGE data sets
• Allpaths-LG results (6.8 GB)
• Bambus2 results (3.1GB)
• CABOG results (5.4 GB)
• MSR-CA results (6.6 GB)
• SGA results (6.3 GB)
• SOAPdenovo results (3.3 GB)
• Velvet results (5.4 GB)
• The above files include BWA read mapping results, the original and RACA assembly, predicted order and orientation of contigs in the original and RACA assembly, N50 and coverage stats., and adjacency errors.
• Perl script for converting a SAM file to RACA input files (1.7 KB)
• The first argument : path to a SAM file (input)
• The second argument : path to a RACA mapping file (will be created)
• The third argument : path to a mapping stats. (mean and stdev) file (will be created)
• 08/19/2014 - A minor bug for handling headers fixed. Thanks Kapila Gunasekera (University of Bern, Switzerland)
• 04/20/2015 - There was a problem handling read orientations for reads with outward direction. Now it has been fixed and the argument for specifying the read orientation has been removed. Thanks Joana Daniela Damas (Royal Veterinary College, University of London)

Contact: Jaebum Kim (Jaebum.Kim@gmail.com)