reapr
universal tool for genome assembly evaluation
Command lineScience
Not tested on a device yet. What that means
Commands in the package
reapr
About reapr
From Debian's package description
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.
The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly.
From Debian's description of the reapr package, under that package's license.
Dependencies
Depends on
Related apps
- roaryhigh speed stand alone pan genome pipelineCommand line
- atacgenome assembly-to-assembly comparisonCommand line
- pilonautomated genome assembly improvement and variant detection toolCommand line
- shastananopore whole genome assembly (binaries and scripts)Command line
- assemblyticsdetect and analyze structural variants from a genome assemblyCommand line
GalvaniReads data from a device with graphical plots and evaluation
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the reapr package, under that package's license.
- Description: Debian's description of the reapr package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.