smalt-examples_0.7.6-4_all.deb


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Description

smalt-examples - Sequence Mapping and Alignment Tool (examples)

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name smalt-examples
Package version 0.7.6
Package release 4
Package architecture all
Package type deb
Installed size 68.60 KB
Download size 68.55 MB
Official Mirror archive.ubuntu.com
SMALT efficiently aligns DNA sequencing reads with a reference genome.
It 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.

Alternatives

Package Version Architecture Repository
smalt-examples_0.7.6-4_all.deb 0.7.6 all Ubuntu Universe
smalt-examples - - -

Download

Type URL
Binary Package smalt-examples_0.7.6-4_all.deb
Source Package smalt

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install smalt-examples deb package:
    # sudo apt-get install smalt-examples

Files

Path
/usr/share/doc/smalt-examples/changelog.Debian.gz
/usr/share/doc/smalt-examples/copyright
/usr/share/doc/smalt/test/SAM.py.gz
/usr/share/doc/smalt/test/bam_cigar_test.py.gz
/usr/share/doc/smalt/test/cigar_test.py
/usr/share/doc/smalt/test/formats.py.gz
/usr/share/doc/smalt/test/ioform_test.py
/usr/share/doc/smalt/test/mthread_test.py
/usr/share/doc/smalt/test/ouform_cigar_test.py
/usr/share/doc/smalt/test/results_split_test.py.gz
/usr/share/doc/smalt/test/sample_test.py.gz
/usr/share/doc/smalt/test/splitReads_test.py
/usr/share/doc/smalt/test/testdata.py.gz
/usr/share/doc/smalt/test/xali_test.py.gz
/usr/share/doc/smalt/test/data/Makefile.am
/usr/share/doc/smalt/test/data/Makefile.gz
/usr/share/doc/smalt/test/data/Makefile.in.gz
/usr/share/doc/smalt/test/data/cigar_read1.fq
/usr/share/doc/smalt/test/data/cigar_read2.fq
/usr/share/doc/smalt/test/data/cigar_ref.fa.gz
/usr/share/doc/smalt/test/data/contigs.fa.gz
/usr/share/doc/smalt/test/data/gen1l100i500e1_1.fq
/usr/share/doc/smalt/test/data/gen1l100i500e1_2.fq
/usr/share/doc/smalt/test/data/gen1l75i300e0_1.fq.gz
/usr/share/doc/smalt/test/data/gen1l75i300e0_2.fq.gz
/usr/share/doc/smalt/test/data/genome_1.fa.gz
/usr/share/doc/smalt/test/data/hs37chrXtrunc.fa.gz
/usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc.bam.gz
/usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc.sam.gz
/usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc_nonam_1.fq.gz
/usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc_nonam_2.fq.gz
/usr/share/doc/smalt/test/data/sequence_test_1.fa.gz
/usr/share/doc/smalt/test/data/sequence_test_2.fa.gz
/usr/share/doc/smalt/test/data/sequence_test_3.fq.gz
/usr/share/doc/smalt/test/data/sequence_test_4.fq.gz

Changelog

See smalt_0.7.6-4_i386.deb changelog.

See Also

Package Description
smalt_0.7.6-4_i386.deb Sequence Mapping and Alignment Tool
smart-notifier_0.28-5_all.deb graphical hard disk health status notifier
smartlist_3.15-25_i386.deb Versatile and Intelligent List Processor
smartpm-core_1.4-2_i386.deb An alternative package manager that works with dpkg/rpm
smartpm_1.4-2_all.deb An alternative package manager that works with dpkg/rpm
smartshine_0.36-0ubuntu2_all.deb Automatic photo adjusting software
smarty-gettext_1.2.0-1ubuntu1_all.deb Gettext plugin enabling internationalization in Smarty
smarty-validate_3.0.3-2_all.deb Server-side form validation plugin for Smarty
smarty3_3.1.21-1ubuntu1_all.deb Template engine for PHP
smb-nat_1.0-6ubuntu1_i386.deb Netbios Auditing Tool
smb2www_980804-41_all.deb SMB/CIFS network client with a web interface
smb4k_1.1.2-1_i386.deb Samba (SMB) share advanced browser for KDE
smbc_1.2.2-4build1_i386.deb samba-commander - curses based samba network browser
smbios-utils_2.3.0-0ubuntu1_i386.deb Provide access to (SM)BIOS information -- utility binaries
smbldap-tools_0.9.9-1ubuntu1_all.deb Scripts to manage Unix and Samba accounts stored on LDAP
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