mira-assembler_3.4.0.1-1_amd64.deb


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Description

mira-assembler - Whole Genome Shotgun and EST Sequence Assembler

Property Value
Distribution Ubuntu 12.04 LTS (Precise Pangolin)
Repository Ubuntu Universe amd64
Package name mira-assembler
Package version 3.4.0.1
Package release 1
Package architecture amd64
Package type deb
Installed size 8.29 KB
Download size 3.59 MB
Official Mirror archive.ubuntu.com
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
specialised on reconstructing pristine mRNA transcripts while
detecting and classifying single nucleotide polymorphisms (SNP)
occuring in different variations thereof.
The assembler is routinely used for such various tasks as mutation
detection in different cell types, similarity analysis of transcripts
between organisms, and pristine assembly of sequences from various
sources for oligo design in clinical microarray experiments.
The package provides the following executables:
Binaries provided:
* mira: for assembly of genome sequences
* miramem: estimating memory needed to assemble projects. Realised through
link to mira.
* convert_project: for converting project file types into other types
* caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
frequently used file converters (realised through links to convert_project)
* scftool: set of tools useful when working with SCF trace files
* fastatool: set of tools useful when working with FASTA trace files
Scripts provided:
* fasta2frag.tcl: fragmenting sequences into smaller, overlapping
subsequences. Useful for simulating shotgun sequences. Can create
subsequences in both directions (/default) and also paired-end sequences.
* fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
a file with names of reads, select the sequences from the input FASTA (and
quality file) and writes them to an output FASTA
* fastqselect.tcl: like fastaselect.tcl, only for FASTQ
* fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
consensus tags in ACE files written by the MIRA assembler (and possibly
other programs). This script massages an ACE file so that consed can read
the consensus tags.

Alternatives

Package Version Architecture Repository
mira-assembler_3.4.0.1-1_i386.deb 3.4.0.1 i386 Ubuntu Universe
mira-assembler - - -

Requires

Name Value
libboost-regex1.46.1 >= 1.46.1-1
libboost-thread1.46.1 >= 1.46.1-1
libc6 >= 2.4
libexpat1 >= 1.95.8
libgcc1 >= 1:4.1.1
libstdc++6 >= 4.6
libtcmalloc-minimal0 -
zlib1g >= 1:1.1.4

Download

Type URL
Binary Package mira-assembler_3.4.0.1-1_amd64.deb
Source Package mira

Install Howto

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

Files

Path
/usr/bin/convert_project
/usr/bin/fasta2frag
/usr/bin/fastaselect
/usr/bin/fastatool
/usr/bin/fastqselect
/usr/bin/fixACE4consed
/usr/bin/mira
/usr/bin/miraSearchESTSNPs
/usr/bin/miraclip
/usr/bin/miramem
/usr/bin/scftool
/usr/bin/sw
/usr/share/doc/mira-assembler/HELP_WANTED
/usr/share/doc/mira-assembler/NEWS.gz
/usr/share/doc/mira-assembler/README
/usr/share/doc/mira-assembler/THANKS
/usr/share/doc/mira-assembler/TODO.Debian
/usr/share/doc/mira-assembler/changelog.Debian.gz
/usr/share/doc/mira-assembler/copyright
/usr/share/mira/demoparam.prm
/usr/share/mira/support_3rdparty_tools/GTAGDB
/usr/share/mira/support_3rdparty_tools/README
/usr/share/mira/support_3rdparty_tools/consedrc.13.0
/usr/share/mira/support_3rdparty_tools/consedtaglib.txt

See Also

Package Description
mira-doc_3.4.0.1-1_all.deb documentation for the mira assembler
mira-examples_3.4.0.1-1_all.deb files to experiment with the mira assembler
mirage_0.9.5.1-1.1_amd64.deb fast and simple GTK+ image viewer
miredo-server_1.2.3-1ubuntu1_amd64.deb Teredo IPv6 tunneling server
miredo_1.2.3-1ubuntu1_amd64.deb Teredo IPv6 tunneling through NATs
mirmon_2.4-2_all.deb monitor the state of mirrors
miro-data_4.0.4-1_all.deb GTK+ based RSS video aggregator data files
miro_4.0.4-1_amd64.deb GTK+ based RSS video aggregator
mirror_2.9-59_all.deb keeps FTP archives up-to-date
mirrorkit_0.1.1-0ubuntu4_all.deb Python frontend to debmirror
mirrormagic-data_2.0.2.0deb1-9_all.deb Data files for mirrormagic
mirrormagic_2.0.2.0deb1-9_amd64.deb Shoot around obstacles to collect energy using your beam
missidentify_1.0-6_amd64.deb a program to find win32 applications
missingh-doc_6_all.deb transitional dummy package
mistelix_0.33-3_amd64.deb DVD authoring and slideshow creation application
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