deb_control_files:
- control
- md5sums
deb_fields:
Architecture: arm64
Depends: libc6 (>= 2.34), libhts3t64 (>= 1.17), zlib1g (>= 1:1.2.2.4)
Description: |-
short read mapping with gaps
Segemehl is a software to map short sequencer reads to reference
genomes. Segemehl implements a matching strategy based on enhanced
suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip'ed
and bgzip'ed). In addition to the alignment of reads from standard DNA-
and RNA-seq protocols, it also allows the mapping of bisulfite converted
reads (Lister and Cokus) and implements a split read mapping strategy.
The output of segemehl is a SAM or BAM formatted alignment file. In the
case of split-read mapping, additional BED files are written to the
disc. These BED files may be summarized with the postprocessing tool
haarz. In the case of the alignment of bisulfite converted reads, raw
methylation rates may also be called with haarz.
.
In brief, for each suffix of a read, segemehl aims to find the
best-scoring seed. Seeds might contain insertions, deletions, and
mismatches (differences). The number of differences allowed within a
single seed is user-controlled and is crucial for the runtime of the
program. Subsequently, seeds that undercut the user-defined E-value are
passed on to an exact semi-global alignment procedure. Finally, reads
with a minimum accuracy of percent are reported to the user.
Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
Installed-Size: '1311'
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Package: segemehl
Priority: optional
Section: science
Source: segemehl (0.3.4-5)
Version: 0.3.4-5+b2
srcpkg_name: segemehl
srcpkg_version: 0.3.4-5