Sequence Assembly/Mapping Programs Now Available on Helix/Biowulf (Helix)

A collection of sequence assembly and mapping programs is now available on Helix and Biowulf for new-generation sequence data such as Solexa, 454, Sanger including:

- The Staden package: a fully developed set of DNA sequence assembly, editing and analysis tools including Gap4 and Spin.
- CAP3: small-scale assembly of EST sequences
- PCAP: large-scale assembly of genomic sequences
- SOAP: efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences
- AMOS: an infrastructure to help users design their own shotgun assembler
- Phred/Phrap/Consed: a suite of programs to read sequencing trace files, call bases, assemble shotgun data, and view/edit finished assemblies.
- MIRA: a whole genome shotgun and EST sequence assembler for 454/Solexa/Sanger data.
- Velvet: a de novo genomic assembler specially designed for short read sequencing technologies such as 454 or Solexa.

For more information, see http://helix.nih.gov/Applications/#_assembly

Please contact staff@helix.nih.gov with any questions.