Miniasm is a very fast OLC-based *de novo* assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. So far miniasm is in early development stage. It has only been tested on a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the mapping step, it takes about 3 minutes to assemble a bacterial genome. Under the default setting, miniasm assembles 9 out of 12 PacBio datasets and 3 out of 4 ONT datasets into a single contig. Miniasm confirms that at least for high-coverage bacterial genomes, it is possible to generate long contigs from raw PacBio or ONT reads without error correction. It also shows that minimap can be used as a read overlapper, even though it is probably not as sensitive as the more sophisticated overlapers such as MHAP and DALIGNER. Coupled with long-read error correctors and consensus tools, miniasm may also be useful to produce high-quality assemblies.
OS | Architecture | Version |
---|---|---|
NetBSD 10.0 | aarch64 | miniasm-0.3.tgz |
NetBSD 10.0 | aarch64 | miniasm-0.3.tgz |
NetBSD 10.0 | aarch64 | miniasm-0.3.tgz |
NetBSD 10.0 | aarch64eb | miniasm-0.3.tgz |
NetBSD 10.0 | aarch64eb | miniasm-0.3.tgz |
NetBSD 10.0 | alpha | miniasm-0.3.tgz |
NetBSD 10.0 | alpha | miniasm-0.3.tgz |
NetBSD 10.0 | sparc64 | miniasm-0.3.tgz |
NetBSD 10.0 | sparc64 | miniasm-0.3.tgz |
NetBSD 10.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 10.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 10.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 10.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 9.0 | aarch64 | miniasm-0.3.tgz |
NetBSD 9.0 | aarch64 | miniasm-0.3.tgz |
NetBSD 9.0 | aarch64 | miniasm-0.3.tgz |
NetBSD 9.0 | alpha | miniasm-0.3.tgz |
NetBSD 9.0 | alpha | miniasm-0.3.tgz |
NetBSD 9.0 | sparc64 | miniasm-0.3.tgz |
NetBSD 9.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 9.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 9.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 9.0 | x86_64 | miniasm-0.3.tgz |
NetBSD 9.3 | x86_64 | miniasm-0.3.tgz |
NetBSD 9.3 | x86_64 | miniasm-0.3.tgz |
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