Table 5. Postprocessing filters (“scaffolders”): Practical and technical comparisons.
| Postprocessing Filters | Operating System | Programming Language | Single PC/Cluster | Open-Source | Paired-End Libraries | Input File Formats | Output File Formats | Websites | Ref. |
| Bumbus2* (V2.0) | Linux, Sun/Solaris Alpha/Ultrix Darwin OS X | C++, Python, Perl | Single | Y | Illumina, 454 | AMOS*** | fasta, agp, dot | http://amos.sf.net | [56] |
| SSPACE* | Linux | Perl | Single | Y (Basic v) N (Premium) | Illumina, 454, SOLiD | fasta/fastq | fasta | www.baseclear.com/bioinformatics-tools/ | [52] |
| SOPRA (V1.4.6) | Linux (64) bits, Mac OS X | Perl | Single | Y | Illumina, SOLiD** | fasta, sam** | fasta** | http://www.physics.rutgers.edu/~anirvans/SOPRA/ | [53] |
| Opera* (V1.3.1) | Linux | Java/C++ | Single | Y | Any platform | fasta****, sam/bowtie | fasta | http://sourceforge.net/projects/operasf | [55] |
| MIP Scaffolder* (V0.5) | Linux (64) bits | C++, Perl | Single | Y | Illumina | fasta, sam | fasta | http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/ | [57] |
| SCARPA* | Linux (64) bits | C++, Perl | Single | Y | Illumina, SOLiD | fasta, sam | fasta | http://compbio.cs.toronto.edu/hapsembler/scarpa.html | [54] |
*
Personal communications with authors.
**
Users' experiences and communities' websites.
***
There are utilities available to import a variety of different data formats into AMOS.
****
For preprocessing, read files can be in fasta/fastq.