Ubuntu
mira package

mira 4.9.5-2 source package in Ubuntu

Changelog

mira (4.9.5-2) unstable; urgency=medium

  * Verify that package builds without problems with gcc-5
    Closes: #793261
  * override false lintian positives
  * Fix spelling
  * wrote missing manpage and moved manpages to separate dir

 -- Andreas Tille <email address hidden>  Fri, 04 Dec 2015 12:56:09 +0100

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

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mira_4.9.5-2.dsc 2.3 KiB 3062e7f07daf97a9b678da715219d64b701de1b20e36f6b20c6e9fdd78b781f4
mira_4.9.5.orig.tar.bz2 10.0 MiB 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77
mira_4.9.5-2.debian.tar.xz 14.4 KiB c778c1f4e02faa79d370299dc518a83e8433019225e4748c92c3a71a3755b0af

No changes file available.

Binary packages built by this source

mira-assembler: Whole Genome Shotgun and EST Sequence Assembler

 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)
 occurring 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: fragmenting sequences into smaller, overlapping
    subsequences. Useful for simulating shotgun sequences. Can create
    subsequences in both directions (/default) and also paired-end sequences.
  * fastaselect: 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: like fastaselect, only for FASTQ
  * fixACE4consed: 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.

mira-assembler-dbgsym: debug symbols for package mira-assembler

 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)
 occurring 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: fragmenting sequences into smaller, overlapping
    subsequences. Useful for simulating shotgun sequences. Can create
    subsequences in both directions (/default) and also paired-end sequences.
  * fastaselect: 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: like fastaselect, only for FASTQ
  * fixACE4consed: 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.

mira-doc: documentation for the mira assembler

 The mira genome fragment assembler is a specialised assembler for
 sequencing projects classified as 'hard' due to high number of similar
 repeats.
 .
 This package contains an HTML book introducing to mira.

mira-examples: files to experiment with the mira assembler

 The mira genome fragment assembler is a specialised assembler for
 sequencing projects classified as 'hard' due to high number of similar
 repeats.
 .
 This package contains a series of files to exploit the functionality
 of mira.