Staden 2.0.0b11

Rodger Staden in Education / Science

Staden screenshot

User Rating: 3.0 (28 votes)

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Features:
Sequence assembly (gap4/gap5)
DNA/Protein analysis (spin)
Sequence alignment
Genome viewer


April 2016 - 2.0.0b11
==========

Gap5 Updates
------------

* Find Haplotypes function for use within the contig editor. This
replaces the old Sort By Sequence mode as well as generating lists
of read IDs per haplotype. It also creates a master "haplotypes"
list of lists.

* Disassemble Readings now handles list of lists (in addition to
normal lists of readings), for use with the haplotype output.

* Improvements to Shuffle Pads. It can now use cutoff/soft-clip
data to detect concordant soft-clips (regions where all the
soft-clip data agrees with one another). It auto-detects likely
adapter sequences to avoid extending these.

It also now detects short tandem repeats and handles these more
carefully. An STR overlapping a heterozygous indel can be clipped
back if the read doesn't span the entire STR, in order to not cause
bias in the copy numbers.

* The Realign Selection option now brings up a user interface if invoked
from the main menu, but not when right clicked via the popup menu
(unless Control key is held down while right-clicking).

* Export Contigs has an additional depadded option to use original
reference sequence coordinates. Note this isn't 100% robust as it
depends on which edits have happened, in particular joining and
breaking contigs.

* Export SAM, BAM and CRAM should now be much faster in excessively
deep regions with soft-clips.

* The quality values can now be overriden when importing FASTQ or the
default quality changed when importing FASTA.

* Gap5_cmd has gained Contig Extend and Contig Trim commands.

* Gap5_cmd auto_join now honours the -min_overlap and -max_overlap
parameters.

* Improved the consensus discrepancy score by taking into account a
per-base difference rather than joining all together.

* Check Assembly text results are now more verbose, for easier
comparison between databases.

* The current selected reading list in the Contig Editor now shows the
number of items in that list.

* Highlight Disagreements for cutoff data now defaults to displaying
foreground coloured differences.

* The consensus algorithm has been tweaked to cope with different
overcall and undercall likelihoods. This is tied to sequencing
technology, for which the default can be adjusted in the Options
menu. This uses the @RG "PL"atform heading in BAM files. The List
Libraries window permits editing of this field after import.

* Small tweaks to Find Internal Joins block alignments.

* Save Consensus can now optionally emit ambiguity codes for
heterozygous positions.

* Added back Mask/Mark consensus filtering modes to Find Internal
Joins.

* Read name indexing should uses less temporary disk space in
tg_index.

* The multi-column reading list viewer now has Template Status and
Library Name columns for display/sorting.

* The Template Display now has hot-keys for configurations. Use
Shift-Function-Key to remember the current settings and Function-Key
to switch to that setting. The File -> Save Settings option will
write these to your ~/.gap5rc.


Gap5 Fixes
----------

* Fixed a bug where using the contig selector / contig list to fill
out a dialogue box without then doing anything else at all could
cause the name to be considered invalid.

* Removed used of some unintialised data in Shuffle Pads.
- Validate_clip_regions could process annotation record numbers that
have been removed already.
- Functions setting sequence clip points could potentially set clips
beyond the sequence ends.

* Fixed a bin corruption caused by updates to read pairs spanning two
contigs, eg with one editor open on each end. (See r3996 for the
long description.)

top download editor's pick
File Size: 20.099609375 MB License: Open Source Price: FREE
Platform: Windows 2000, Windows 2003, Windows XP, Windows Vista, Windows Vista x64, Windows 7, Windows 7 x64, Windows 8, Windows 8 x64, Windows 10, Windows 10 x64, Linux, Mac OS X
Downloads: Total: 137 | This Month: 15 Released: 2016-04-25
Staden Similar Software

DNA Counter 1.1 Heracle BioSoft    

... will show the proportions between nucleotides in a DNA sequence. You don't need to install it or ... to run it. Other software by Heracle BioSoft: DNA Baser is an affordable alternative for assembly of DNA sequences and generation of contigs. File formats supported .... Free download of DNA Counter 1.1

BVTech Plasmid(1) 5.0 BV Tech, Inc.    

BVTech Plasmid is DNA sequence analysis and plasmid drawing software for Windows PCs.You can use it to plan your DNA cloning, draw high quality plasmid maps, analyse your DNA sequencing data, align sequences, convert sequence formats among EMBL, GeneBank, FASTA, IG, .... Free download of BVTech Plasmid(1) 5.0

Unipro UGENE 1.27.0 Unipro    

... UGENE is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools ... and integration with REBASE; Extremely fast repeat finder; DNA short reads to reference alignment using Bowtie; De novo assembly with CAP3; Search for transcription factor binding sites using SITECON; Protein back translation; ORF .... Free download of Unipro UGENE 1.27.0

Unipro UGENE for Mac 1.16.2 Unipro    

... Mac is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools ... and integration with REBASE; Extremely fast repeat finder; DNA short reads to reference alignment using Bowtie; De novo assembly with CAP3; Search for transcription factor binding sites using SITECON; Protein back translation; ORF .... Free download of Unipro UGENE for Mac 1.16.2

Unipro UGENE for Linux 1.16.2 Unipro    

... Linux is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools ... and integration with REBASE; Extremely fast repeat finder; DNA short reads to reference alignment using Bowtie; De novo assembly with CAP3; Search for transcription factor binding sites using SITECON; Protein back translation; ORF .... Free download of Unipro UGENE for Linux 1.16.2

Popular Software in Education / Science

STL Tracker 2.5.0.14 Sumus Technology Limited     update

The next generation of satellite tracking software for Windows. Free download of STL Tracker 2.5.0.14

AstroGrav for Mac 3.7.1 AstroGrav Astronomy Software     update

A high precision solar system simulator/calculator with interactive 3D viewing.. Free download of AstroGrav for Mac 3.7.1

AstroGrav 3.7.1 AstroGrav Astronomy Software     update

A high precision solar system simulator/calculator with interactive 3D viewing.. Free download of AstroGrav 3.7.1

Stellarium for Linux 0.19.0.1 Stellarium     update

Stellarium is a free open source planetarium for your computer. Free download of Stellarium for Linux 0.19.0.1

software pick   

Stellarium 0.19.0.1 Stellarium     update

Stellarium is a free open source planetarium for your computer. Free download of Stellarium 0.19.0.1

software pick