mira 4.9.5-4 source package in Ubuntu
Changelog
mira (4.9.5-4) unstable; urgency=medium * Packaging moved from SVN to Git * Loosen boost dependencies. -- Michael R. Crusoe <email address hidden> Tue, 02 Feb 2016 00:45:21 -0800
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 | Published | Component | Section |
|---|
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| mira_4.9.5-4.dsc | 2.4 KiB | 354a4e1283e4dae85f5d44b131695353ee5d282958f3d3d60896a0939c91cae0 |
| mira_4.9.5.orig.tar.bz2 | 10.0 MiB | 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77 |
| mira_4.9.5-4.debian.tar.xz | 18.9 KiB | 9490a75f62cb736c77c6b19db3e4bc5b469a604b85e833656cad5c8056c5ebc7 |
Available diffs
- diff from 4.9.5-3 to 4.9.5-4 (6.7 KiB)
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.
