shasta
nanopore whole genome assembly (binaries and scripts)
Command lineScience
Not tested on a device yet. What that means
Commands in the package
shasta
About shasta
From Debian's package description
De novo assembly from Oxford Nanopore reads. The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.
Computational methods used by the Shasta assembler include:
- Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
- Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).
Shasta assembly quality is comparable or better than assembly quality achieved by other long read assemblers.
This package contains the executable binaries (tools) and accommodating scripts.
From Debian's description of the shasta package, under that package's license.
Dependencies
Depends on
libboost-chrono1.83.0t64libboost-program-options1.83.0libc6libgcc-s1libstdc++6python3-shasta
Related apps
- plinkwhole-genome association analysis toolsetCommand line
- roaryhigh speed stand alone pan genome pipelineCommand line
- mira-assemblerWhole Genome Shotgun and EST Sequence AssemblerCommand line
- atacgenome assembly-to-assembly comparisonCommand line
- mcallerfind methylation in nanopore readsCommand line
- plink2whole-genome association analysis toolsetCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the shasta package, under that package's license.
- Description: Debian's description of the shasta package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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