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From: Rahul S. <rah...@gm...> - 2012-02-21 15:39:03
|
Dear all, I have merged two velvet assemblies using minimus2 and now I have .contig and .bnk/ files, I want to do scaffolding of these generated contigs using goBambus2. As goBambus2 requires .mate file, how can I generate this file? I did my assemblies from Illumina paired-end reads. Is this .mate file refer to that pair information? I read number of forums but didi not get any solution. Can anybody please suggest me how can I proceed further? Best regards, Rahul -- Rahul Sharma, Ph.D Scholar, Senckenberg Research Institute and Nature Museum Biodiversity and Climate Research Centre LOEWE BiK-F Senckenberganlage 25 D-60325 Frankfurt am Main, Germany |
From: Rahul S. <rah...@gm...> - 2012-02-08 17:26:16
|
Dear Amos users, I have 4-5 nice velvet assemblies from different k-mers. I want to merge all these assemblies into a single one. I have following queries regarding the minimus2 usage: 1). Is it possible to merge all these 5 assemblies into a single one? 2). I was trying Minimus and getting blank .fasta and .contig files. What could be the reason behind this? Is there any test dataset on which I can run Minimus2 and Minimus2-Blat? 3). I am working on the Scaffolded sequences which have N's, from the Amos page, I read that the amos-3.1.0 version can support N's. Should I try minimus2 with or without Scaffolding, according to your experience? I would appriciate your comments, Best Regards, Rahul -- Rahul Sharma, Ph.D Scholar, |
From: Michael S. <ms...@um...> - 2009-07-13 00:53:46
|
Hi AMOS users, Just a quick announcement to say the AMOS documentation has moved into a wiki hosted at sourceforge. The main AMOS URL (http://amos.sourceforge.net) and the URLs for the published components (Figaro, Hawkeye, Forensics, Minimus, AMOScmp, ABBA) redirect to their new locations inside the wiki, but other deep links you bookmarked may be broken. The documentation was relocated with only minor editing, but we are planning more extensive edits for the summer. Our hope is this migration will make it easier to keep the pages up to date and complete. Thank you for your support! Michael Schatz |
From: Michael S. <ms...@um...> - 2006-11-01 22:22:33
|
AMOS 2.0.0 November 1, 2006 ---------------- The AMOS developers are proud to announce version 2.0.0 of the modular open source assembler package AMOS. Version 2.0.0 brings a new level of quality, performance, and capabilities to the AMOS suite. In addition to creating and enhancing the tools in this release, we made significant improvements to the core AMOS library to greatly increase the performance of almost every tool. We encourage all users to upgrade from the previous versions. Download the AMOS 2.0.0 source package at: http://prdownloads.sourceforge.net/amos/amos-2.0.0.tar.gz?download Version 2.0.0 is a major upgrade over the previous release, but we worked hard to ensure there were no changes to break binary or message compatibility, so your old AMOS banks and message files can be read without any translation. However, we have standardized on the .bnk suffix for banks so you may need to update your code if you use minimus or AMOScmp and expected the .bank suffix. As mentioned above, the first change that you will notice is greatly improved performance in many of the tools. This was accomplished by streamling and optimizing the Bank IO, and adding new methods to read just the fixed store. This enables the viewer, for example, to index the reads without loading their sequences, thus drastically reducing the time it takes to open a bank. Other tools, such as minimus saw additional performance improvements by optimizing the algorithms used. The performance of the hash-overlap algorithm, for example, has been greatly improved on repetitive sequences by computing multiple banded alignments rather than potentially computing the entire scoring matrix. We are also proud to announce Hawkeye 1.0. Hawkeye, formerly known as bankViewer or the Assembly Investigator, is a interactive visual assembly analysis tool that allows one to inspect all aspects of an assembly. It was designed to aid in diagnosing global assembly problems or localized mis-assemblies. All of the old functionality of bankViewer/Assembly Investigator, especially the Scaffold and Contig views of the data, are still present, but this version also includes a new Assembly Launch Pad which provides a global overview of your assembly. The initial display shows the sizes and quality of your assembly at a glance, and other tabs allow for systematic inspection and analysis of the libraries, scaffolds, contigs, reads, and inserts in your assembly. For more details, check out Hawkeye's website at: http://amos.sourceforge.net/hawkeye There has been quite a bit of discussion on the mailing list and forums lately. We strongly encourage you to sign up as well: https://lists.sourceforge.net/lists/listinfo/amos-help Important URLs -------------- Website: http://amos.sourceforge.net Documentation: http://amos.sourceforge.net/docs Download: http://sourceforge.net/project/showfiles.php?group_id=134326&package_id=147480 Mailing List: https://lists.sourceforge.net/lists/listinfo/amos-help Core AMOS API Changes --------------------- BankStream: Add methods to just read the fixed store information, greatly improving performance when streaming through data IDMap: Optimize reading the name map, EIDs are now restricted to 2048 characters. Significant Tool Updates ------------------------ Hawkeye Version 1.0: Implement launchpad, countless other improvements amosvalidate: Scan assembly for mis-assembly signatures, including mate happiness, SNPs, singleton read alignments, and read coverage analysis minimum(hash-overlap): greatly improved performance tarchive2amos: Convert assembly archive data into AMOS format New Tools --------- casm-breaks: Analyze alignments of reads to a genome to locate potential mis-assemblies select-reads: Specify inclusive or exclusive lists of reads to extract from a bank, along with their mates count-kmers: Count the kmers present in a multi-fasta file, or in read or contig banks kmer-cov-plot: Show the kmer-coverage at each position along a multi-fasta file insert-sizes: Compute the size of each insert in the assembly library-histogram: Compute the mean/stdev of each libary, and display a histogram ce-statcov: Compute Compression/Expansion (CE) statistic at each position in assembly shotgunSim: Assembly simulator drawing inserts from parameterized libraries tandemCollapse: Simulate the collapse of tandem repeat in a previously generated layout Full change log at: http://sourceforge.net/project/shownotes.php?release_id=460226&group_id=134326 Thank You, Michael Schatz AMOS Project Administrator Center for Bioinformatics and Computational Biology University of Maryland |
From: Michael S. <ms...@um...> - 2006-04-14 05:12:07
|
AMOS 1.4.5 April 14, 2006 --------------------- This release incorporates an entirely new view type for the viewer that we call the SNP Barcode. It is a form of semantic zooming so that as you zoom out from displaying individual base pairs, it switches to displaying just the positions with SNPs in your assemblies within several kbp of sequence at a time. You can also visualize the quality values and sequencing error over entire reads. To access it, click on the font decrease (A-) button a few times in the contig tiling display and the view will automatically change once you pass below a threshold. I recently gave a talk about the viewer at TIGR that you may find informative about this feature and the other capabilities of the viewer. You can see the slides for the talk on my webpage at: http://www.cbcb.umd.edu/~mschatz/ The other exciting viewer news is OS X and Cygwin are now supported. See the INSTALL file for details on building on those platforms. If you have problems building the viewer on OS X, I have also created a binary that is statically linked to Qt that will run without any compilation of Qt. The statically linked version does have some Qt/Mac issues causing the coloring of some text to be distorted, but is otherwise quite usable. You should still download and build the source release, though, so you can get the rest of the AMOS tools and converters. Finally, we are proud to annouce a new output mode for bank2contig (-T) that allows any contigs in AMOS to be directly converted into the native XML format for the tool DNPTrapper created by our collaborators at the Karolinska Institute in Sweden. DNPTrapper allows one to visualize the SNPs in an assembly similiar to the SNP Barcode mode of the AMOS Assembly Investigator, but also interact with the assembly by dragging and dropping reads to manually correct misassembled repeats. More information on DNPTrapper is available at: http://dnptrapper.sourceforge.net/ Stay tuned for more significant viewer developments and other AMOS improvements over the next month. Michael Schatz AMOS Project Administrator Center for Bioinformatics and Computational Biology University of Maryland Download AMOS from: http://amos.sourceforge.net/#download Significant Tool Updates ------------------------ Viewer: . SNP Barcode mode . Polish Main Window display . Tint CE Statistic at +/- 3 . Beta OS X & Cygwin Compatibility . Fixed segfault with coverage out of range errors bank2contig: . Support output to DNPTrapper Format (use bank2contig -T) make-consensus: . New option to run only on selected layouts New Tools --------- amosvalidate: Validate AMOS assemblies in afg format. listGCContent: Compute the GC content of reads or contigs. |
From: Michael S. <mic...@gm...> - 2006-01-12 22:17:09
|
I just made some changes to the Viewer. The most significant is how matepairs are classified in the Insert View when a read is present in the current scaffold, but it's mate is not. The viewer used to classify into 'Missing' or 'Linking' based on the position of the read within the scaffold. This was a confusing ad hoc scheme, and can be inferred by distance to the edge of the scaffold. Instead it now classifies into 'Linking Mate' or 'Singleton Mate' based on how the mate is in the assembly. An insert is 'Linking' if the two mated reads are within different scaffolds, and is considered 'Singleton' if the corresponding matepair is not within any contig (or scaffold). Linking mates are evidence for a twisted scaffold or assembler bugs, while Singleton mates are problably just trimming issues or other sequencing error. Note as before there is a third category for Unmated reads colored cyan. Linking Mates are magenta by default, and Singleton mates are yellow. In addition, on the Options menu there is a new option for "Color By Linked Contig", which colors Linking mates by the contig they link to. For example, in LinkingMates-before.png, there are several magenta mates at the bottom, but it doesn't if they link to the same contig or to totally different contigs. Switching to "Color By Linked Contig" shows 4 cyan mates near 42kbp, meaning all 4 of those mates belong to the same contig. (LinkingMates-after.png) The coloring cycles through a 16 color palette, so there could be other cyan mates far away, but the color coding will be accurate locally. As another new feature, Control+Click now takes you to and highlights the mate of the read you click on, even if it is in a different scaffold. Linked.png shows the result of control-clicking that all of the mates within the original contig are within a small 4 read. Here the mates are all green because they all point back to the original contig. The other major change was an overhaul to how the read tiling is drawn to include clipping so extremely deep coverage will still be responsive. For example, it is now possible to scroll through the 1500x coverage on the Entamoeba plasmid. Otherwise, there should be no visible change to how the tiling is displayed. The changes are checked into sourceforge CVS and the new viewer was installed in /fs/sz-user-supported for CBCB users. Please let me know if you encounter any problems or have any questions. -Mike |
From: Adam P. <ada...@ya...> - 2005-06-17 23:39:39
|
Hi all! A *very* quick AMOS update. Version 1.3.1 has been released to fix a couple of small problems. Most notably, fixes for OSX and gcc4.0 users who were having build problems. Also, a couple configure options were added to deal with unusual Qt installs where the qt3 directory does not contain the usual include, bin and lib subdirs, see the README for more info. Finally, the AMOScmp script was changed to call some new program names and to use a new FastA file generator. Any custom AMOScmp scripts will need to be rewritten to abide by these name changes. Diff the new script with your old scripts to see the changes. Best, Adam Phillippy AMOS Sourceforge Administrator __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: Adam P. <ada...@ya...> - 2005-03-22 02:25:59
|
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