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GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed.
Basically, GenSeed-HMM performs three operations, repeatedly:
- recruit reads by matching them to a seed
- assemble the recruited reads (including previously assembled contigs)
- generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs
The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity.
This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used.
Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss.
Features
- progressive assembly
- seed-driven assembly
- large choice of assemblers
- seeds can be profile HMMs, DNA or protein
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