Features

• Circular and linear views of genomes

• Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

• Smooth zooming down to the sequence level

• Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

• Save high resolution PNG maps up to 8000x8000px

• Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

Know of any other open source software for PacBio data? Email us.

Software categories:

• De novo assembly
• Structural Variations Detection
• Reference-based alignment
• Consensus and variant calling
• RNA analysis
• Epigenetic base modifications and methylation
• Barcoding
• Genome Browsers
• Run QC
• Frameworks and APIs

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

Our work is published in Scientific Reports:

Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci. Rep. 6, 31900; doi: 10.1038/srep31900 (2016).

http://www.nature.com/articles/srep31900

The manual can be downloaded from:

https://github.com/yechengxi/DBG2OLC/raw/master/Manual.docx

To use precompiled versions,please go to:

https://github.com/yechengxi/DBG2OLC/tree/master/compiled

Address of the bookmark: https://github.com/yechengxi/DBG2OLC

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

CABOG is one of many software programs called genome assemblers. These programs exist to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of letters long from the hundreds of letters per read that modern sequencers provide. What these programs do is often described as a scaled up version of a family solving a jigsaw puzzle.

The CABOG software was the first to accomplish many scientific goals. It was the first to assemble the genome of a multicellular organism (Drosophila melanogaster, 2000). It was the first to assemble both parental haplotypes of one human genome (J. Craig Venter, 2007). It was the first to assemble environmental sequence from the oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It was first to combine reads from first-generation Sanger sequencing machines and second-generation pyrosequencing machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.

Address of the bookmark: http://www.jcvi.org/cms/research/projects/cabog/overview/

Contact:
Computer Science Building (Science Park 3)
Altenberger Str. 69, A-4040 Linz, Austria
Tel. +43 732 2468 4520 / Fax +43 732 2468 4539
E-mail secretary@bioinf.jku.at

http://www.bioinf.jku.at/

The project is on bacterial gene gain and loss and emerging pathogenicity, and is described in full here: https://www.ebi.ac.uk/research/postdocs/ebpods/projects/goldman-welch-2015 . The EMBL-EBI / Cambridge Computational Biomedical Postdoctoral (“EBPOD”)

The closing date for applications is 3 September 2015. Nick Goldman EMBL-European Bioinformatics Institute Nick Goldman

More at https://www.ebi.ac.uk/research/postdocs/ebpods/projects/goldman-welch-2015

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

 New Features in Genome Workbench 2.7.15

• Multiple Alignment View: implemented adaptive feature display when zooming in
• Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
• Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

• Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
• Multiple Pane View: fixed crash on loading BLAST results
• Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
• Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
• Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
• Text View / Flat File: fixed Mac OS rendering issues
• Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
• File Import: optimization improvement to speed up load of files containing multiple project items
• File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
• Mac OS: improved tooltips for toolbar buttons
• Phylogenetic Tree Builder Tool: improved diagnostics of errors
• Multiple Alignment View: optimizations to avoid main GUI freezes
• Open Dialog: removed duplicate elements in table of genomes (load Genome)
• PDF export: fixed issue with XREF table errors
• Tree View: fixed issues with showing Force Layout progress on Mac OS
• Tree View: PDF export fixed issues for showing labels of collapsed nodes
• Tree View: added an option to stop layout
• Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

https://liulab-dfci.github.io/software/

We are looking for a motivated candidate for handling proteomic and/or transcriptomic and other data with a strong background in bioinformatics tools and database development. The project will include identification of novel peptides from mass spectrometry-based proteomic data.

Familiarity with statistical tools or wet lab experience will be an added advantage. The position is open for immediate appointment and available for two years. The applicant will be appointed as Research Associate or Senior Research Fellow based on qualifications as detailed below:

Research Associate: Ph.D. in Biological Science or Bioinformatics with relevant publications in peer reviewed journals. Familiarity with bioinformatics tools, database development, programming skills and proteomic and/or other omics data analysis. Salary will be as per ICMR rules and guidelines.

Senior Research Fellow: M.Sc./B.Tech. in any branch of biology/ biotechnology/bioinformatics, with minimum 2 years of research experience (essential). Familiarity with bioinformatics tools, database development, programming skills and proteomic data analysis. Salary will be as per ICMR rules and guidelines.

Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: ravi@ibioinformatics.org on or before May 15th, 2014.

Contact:
Dr. Ravi Sirdeshmukh
Distinguished Scientist & Associate Director, IOB,
Principal Advisor MSMC/MSCTR

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