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Source: kmer
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Afif Elghraoui <afif@debian.org>
Section: science
Priority: optional
Build-Depends:
debhelper (>= 10),
dh-exec,
# For ATAC
dh-python,
python-all-dev,
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmer.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/kmer.git
Homepage: http://kmer.sourceforge.net
Package: kmer
Architecture: all
Depends: ${misc:Depends},
meryl,
leaff,
sim4db,
atac,
Description: suite of tools for DNA sequence analysis
The kmer package is a suite of tools for DNA sequence analysis.
It provides tools for searching (ESTs, mRNAs, sequencing reads);
aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
based on kmers.
.
This is a metapackage depending on the executable components of the kmer suite.
Package: libkmer-dev
Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
libmeryl-dev
Description: suite of tools for DNA sequence analysis (development lib)
The kmer package is a suite of tools for DNA sequence analysis.
It provides tools for searching (ESTs, mRNAs, sequencing reads);
aligning (ESTs, mRNAs, whole genomes); and a variety of analyses
based on kmers.
.
This package contains headers and static libraries for kmer.
Package: meryl
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: gridengine-client
Description: in- and out-of-core kmer counting and utilities
meryl computes the kmer content of genomic sequences. Kmer
content is represented as a list of kmers and the number of
times each occurs in the input sequences. The kmer can be
restricted to only the forward kmer, only the reverse kmer,
or the canonical kmer (lexicographically smaller of the
forward and reverse kmer at each location). Meryl can
report the histogram of counts, the list of kmers and their
counts, or can perform mathematical and set operations
on the processed data files.
.
This package is part of the Kmer suite.
Package: libmeryl-dev
Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends}
Description: in- and out-of-core kmer counting and utilities (development lib)
meryl computes the kmer content of genomic sequences. Kmer
content is represented as a list of kmers and the number of
times each occurs in the input sequences. The kmer can be
restricted to only the forward kmer, only the reverse kmer,
or the canonical kmer (lexicographically smaller of the
forward and reverse kmer at each location). Meryl can
report the histogram of counts, the list of kmers and their
counts, or can perform mathematical and set operations
on the processed data files.
.
This package contains the static libraries and header files.
Package: leaff
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Description: biological sequence library utilities and applications
LEAFF (Let's Extract Anything From Fasta) is a utility program for
working with multi-fasta files. In addition to providing random access
to the base level, it includes several analysis functions.
.
This package is part of the Kmer suite.
Package: sim4db
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Recommends: leaff
Description: batch spliced alignment of cDNA sequences to a target genome
Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence
sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc
algorithms to determine the alignments, but incorporates a fast sequence
indexing and retrieval mechanism, implemented in the sister package
'leaff', to speedily process large volumes of sequences.
.
While sim4db produces alignments in the same way as sim4 or sim4cc, it
has additional features to make it more amenable for use with whole-genome
annotation pipelines. A script file can be used to group pairings between
cDNAs and their corresponding genomic regions, to be aligned as one run
and using the same set of parameters. Sim4db also optionally reports more
than one alignment for the same cDNA within a genomic region, as long
as they meet user-defined criteria such as minimum length, percentage
sequence identity or coverage. This feature is instrumental in finding
all alignments of a gene family at one locus. Lastly, the output is
presented either as custom sim4db alignments or as GFF3 gene features.
.
This package is part of the Kmer suite.
Package: atac
Architecture: any
Depends:
${shlibs:Depends},
${misc:Depends},
${python:Depends},
${perl:Depends},
libfile-which-perl,
leaff,
meryl,
gnuplot,
Description: genome assembly-to-assembly comparison
atac computes a one-to-one pairwise alignment of large DNA sequences. It first
finds the unique k-mers in each sequence, chains them to larger blocks, and
fills in spaces between blocks. It was written primarily to transfer
annotations between different assemblies of the human genome.
.
The output is a set of ungapped 'matches', and a set of gapped 'runs' formed
from the matches. Each match or run associates one sequence with the other
sequence. The association is 'unique', in that there is no other (sizeable)
associations for either sequence. Thus, large repeats and duplications are not
present in the output - they appear as unmapped regions.
.
Though the output is always pairwise, atac can cache intermediate results to
speed a comparisons of multiple sequences.
.
This package is part of the Kmer suite.
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