segemehl 0.3.4-5 source package in Ubuntu
Changelog
segemehl (0.3.4-5) unstable; urgency=medium * Team Upload. * d/p/arm64.patch: Fix segfaults on !amd64 and !i386 * Bump Standards-Version to 4.6.0 (no changes needed) -- Nilesh Patra <email address hidden> Tue, 24 Aug 2021 22:19:01 +0530
Upload details
- Uploaded by:
- Debian Med
- Uploaded to:
- Sid
- Original maintainer:
- Debian Med
- Architectures:
- any
- Section:
- misc
- Urgency:
- Medium Urgency
See full publishing history Publishing
| Series | Published | Component | Section | |
|---|---|---|---|---|
| Mantic | release | universe | misc | |
| Lunar | release | universe | misc | |
| Jammy | release | universe | misc |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| segemehl_0.3.4-5.dsc | 2.0 KiB | b3b9a58839fa46fe4705a1d89de8ca7651122ee4001a0b8857b422876dfb9f95 |
| segemehl_0.3.4.orig.tar.xz | 238.4 KiB | e498fb23e36d45a0d0035105812a747ca901af366d07dde431c25a49ee28abbc |
| segemehl_0.3.4-5.debian.tar.xz | 7.6 KiB | 2215ecca17c8dc76082b2e4b45938d981373bac5a122d4afd3abe6dfcd0620ca |
Available diffs
- diff from 0.3.4-3 to 0.3.4-5 (2.8 KiB)
No changes file available.
Binary packages built by this source
- segemehl: 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.
- segemehl-dbgsym: debug symbols for segemehl
