EvoPipes.net serves evolutionary bioinformatic pipelines to examine patterns of gene duplication, identify orthologs, clean next-gen sequence data sets, and more. The site also hosts forums to discuss pipeline results, questions about ecological and evolutionary genomic analyses, and bioinformatics in general. Feel free to upload your data and start getting results today!
Scaffolded and Corrected Assembly of Roche 454
A next-gen sequence assembly tool for evolutionary genomics. Designed especially for assembling 454 EST sequences against high quality reference sequences from related species.
SCARF was created in order to knit together low-coverage 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. SCARF is especially well suited for non-contiguous or low depth data sets such as EST (expressed sequence tag) libraries. SCARF can also be used to sort and assemble a pool of 454 sequence data according to a set of reference sequences (e.g. for metagenomics). See the documentation for a full description of the methodology behind SCARF.
To sign up to the SCARF announcement list send an e-mail to firstname.lastname@example.org with "subscribe" in the subject.
SCARF is free (as in beer and speech) and is licensed under the terms of the GNU General Public License.
Barker, M. S., K. M. Dlugosch, A. C. C. Reddy, S. N. Amyotte, and L. H. Rieseberg. 2009. SCARF: Maximizing next-generation EST assemblies for evolutionary and population genomic analyses. Bioinformatics 25(4): 535-536.
Minimum system requirements:
- GCC 4.2.3 or later (only for compilation)
- 4GB RAM (increases with data set size)
- Local BLAST package available from NCBI
SCARF Source - Source code for compilation
SCARF Linux 32 - Pre-compiled 32 bit Intel x86 Linux (Ubuntu 8.04)
SCARF Linux 64 - Pre-compiled 64 bit Intel x86 Linux (Ubuntu 8.04)
***SCARF is not currently supported on OS X***
Repeat counter for assessing homopolymer run distributions
- Segfault with only one fasta entry in reference file. The current version of SCARF will segfault if the reference file does not contain two or more fasta entries. A fix is in progress, but a working solution is to simply add a "dummy" second fasta entry to the reference file.
- Segfault after megablast step. Generally this occurs because of too little RAM to build all the threads for the scarfing steps. If you are confident that you have enough RAM, please send us a message if you get a segfault.