Ubuntu
smalt package

smalt 0.7.6-9 source package in Ubuntu

Changelog

smalt (0.7.6-9) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]
  * Use 2to3 to port to Python3
    Closes: #938501
  * debhelper-compat 12
  * Standards-Version: 4.4.1
  * Remove trailing whitespace in debian/changelog
  * Use secure URI in debian/watch.
  * Use secure URI in Homepage field.
  * Set upstream metadata fields: Archive, Bug-Submit.
  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g

  [ Michael R. Crusoe ]
  * Fixed the remaining Python3 issues in test scripts

 -- Michael R. Crusoe <email address hidden>  Fri, 03 Jan 2020 11:44:39 +0100

Upload details

Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
any all
Section:
misc
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section
Focal release universe misc

Downloads

File Size SHA-256 Checksum
smalt_0.7.6-9.dsc 2.0 KiB 04467f45b2527fff40dbfee2441fa5d9d26794ced70f11b75a1d9a6c33ff52b9
smalt_0.7.6.orig.tar.gz 68.9 MiB 89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31
smalt_0.7.6-9.debian.tar.xz 8.6 KiB c6e7a6c2864ed46919540d4ec094b169047bf0a047e0556c63174822682ffd79

Available diffs

No changes file available.

Binary packages built by this source

smalt: Sequence Mapping and Alignment Tool

 SMALT efficiently aligns DNA sequencing reads with a reference genome.
 Reads from a wide range of sequencing platforms, for example Illumina,
 Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
 paired reads.
 .
 The software employs a perfect hash index of short words (< 20
 nucleotides long), sampled at equidistant steps along the genomic
 reference sequences.
 .
 For each read, potentially matching segments in the reference are
 identified from seed matches in the index and subsequently aligned with
 the read using a banded Smith-Waterman algorithm.
 .
 The best gapped alignments of each read is reported including a score
 for the reliability of the best mapping. The user can adjust the
 trade-off between sensitivity and speed by tuning the length and spacing
 of the hashed words.
 .
 A mode for the detection of split (chimeric) reads is provided.
 Multi-threaded program execution is supported.

smalt-dbgsym: debug symbols for smalt
smalt-examples: Sequence Mapping and Alignment Tool (examples)

 SMALT efficiently aligns DNA sequencing reads with a reference genome.
 Reads from a wide range of sequencing platforms, for example Illumina,
 Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
 paired reads.
 .
 The software employs a perfect hash index of short words (< 20
 nucleotides long), sampled at equidistant steps along the genomic
 reference sequences.
 .
 For each read, potentially matching segments in the reference are
 identified from seed matches in the index and subsequently aligned with
 the read using a banded Smith-Waterman algorithm.
 .
 The best gapped alignments of each read is reported including a score
 for the reliability of the best mapping. The user can adjust the
 trade-off between sensitivity and speed by tuning the length and spacing
 of the hashed words.
 .
 A mode for the detection of split (chimeric) reads is provided.
 Multi-threaded program execution is supported.
 .
 This package contains example data and a test suite to test the data.