mira 4.9.5-3 source package in Ubuntu

Changelog

mira (4.9.5-3) unstable; urgency=medium

  * Remove *.cc files that are created by old flex version which breaks
    build otherwise
    Closes: #812681

 -- Andreas Tille <email address hidden>  Wed, 27 Jan 2016 13:19:53 +0100

Upload details

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

See full publishing history Publishing

Series Pocket Published Component Section

Downloads

File Size SHA-256 Checksum
mira_4.9.5-3.dsc 2.3 KiB 004d0c08ecf90344c9b6add886eefdb0200ea4c56a17a7769373d48b6210fefd
mira_4.9.5.orig.tar.bz2 10.0 MiB 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77
mira_4.9.5-3.debian.tar.xz 14.5 KiB c0351c87ac9424c3de3e2e4306448397e55a833a9cfedbb4ca414d857856a927

Available diffs

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.