seer
genomic sequence element (kmer) enrichment analysis
Command lineScience
Not tested on a device yet. What that means
Commands in the package
seerR_mdsblast_top_hitsblastn_to_phandangocombineKmersfilter_seerhits_to_fastqkmdsmap_backmapping_to_phandangomash2matrixreformat_output
About seer
From Debian's package description
Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics.
From Debian's description of the seer package, under that package's license.
Dependencies
Depends on
libarmadillo14libblas3orlibblas.so.3libboost-program-options1.83.0libc6libgcc-s1libgzstream0libhdf5-310libstdc++6zlib1glibtext-csv-perl
Related apps
- QGIS DesktopGeographic Information System (GIS)
- ncbi-blast+next generation suite of BLAST sequence search toolsCommand line
- QMapShackGPS mapping (GeoTiff and vector) and GPSr management
- ea-utilscommand-line tools for processing biological sequencing dataCommand line
- hmmerprofile hidden Markov models for protein sequence analysisCommand line
- 4ti2mathematical tool suite for problems on linear spaces -- toolsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the seer package, under that package's license.
- Description: Debian's description of the seer 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.