Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.

Usage

java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)

Options

• -h help; This screen.
• -R (indexed reference file) REQUIRED.
• -u (unmapped chromosome name): default:Unmapped
• -e | --empty : generate EMPTY bams for chromosome having no read mapped
• -m | --mock : if option '-e', add a mock pair of sam records to the empty bam
• -p (output file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam
• -s assume input is sorted.
• -x | --index create index.
• -t | --tmp (dir) tmp file directory
• -G (file) chrom-group file (see below)

Address of the bookmark: https://code.google.com/archive/p/jvarkit/wikis/SplitBam.wiki

To use CLgenomics, individual genome data (genome sequences + annotation details) are compiled and saved in a specially formatted file called CLG (ChunLab Genomics). Each CLG file corresponds with one bacterial genome. If multiple genomes are being considered and compared, multiple CLG files are needed. ChunLab offers >40,000 CLG files of publicly available Bacterial and Archaeal genomes.

Address of the bookmark: https://chunlab.wordpress.com/clgenomics-software/

Samtools

Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format

BCFtools

Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

HTSlib

A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Address of the bookmark: http://www.htslib.org/

A walk-in-interview will be held on 15.7.2013 at 12 noon in the Department of Biophysics, Molecular Biology and Bioinformatics, 92 A.P.C Road, Kolkata-700 009 to select one trainee research fellow and two students under DIC. The positions are purely temporary and would be for a period of six months from the date of joining which may be extended by another six months subject to successful performance.

Qualification:

For the Trainee Research Fellow: Should have a master degree in Bioinformatics or allied subjects and should have biological database development experience. Must have at least one publication.

For the Students: Should have a master degree in Bioinformatics or allied subjects and should be proficient in C-programming language. Must be familiar with techniques of Developmental Biology.

The Trainee Research Fellow would be paid a consolidated sum of Rs 10000/- per month and the students would be paid a sum amount Rs. 7000/- per month during the tenure of the project.

Advertisement:
www.caluniv.ac.in/News%20&%20Announcement/trainee_rf_DIC.pdf

JSON is built on two structures:

• A collection of name/value pairs. In various languages, this is realized as an object, record, struct, dictionary, hash table, keyed list, or associative array.
• An ordered list of values. In most languages, this is realized as an array, vector, list, or sequence.

These are universal data structures. Virtually all modern programming languages support them in one form or another. It makes sense that a data format that is interchangeable with programming languages also be based on these structures.

Address of the bookmark: http://json.org/

The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He/she will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.

Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to joets@moulon.inra.fr.

 All the nodes in the tree are clickable. This displays various information and options:

• The species name (and the associated common name if there is one)
• The rank (kingdom, family, class, species...)
• Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)
• Possibility to download the corresponding subtree in newick extended format
• Possibilty to get the whole lineage from the current node/tip to the root of the tree.

Address of the bookmark: http://lifemap-ncbi.univ-lyon1.fr/

Research Area

the discovery and on-demand use of biomedical data and services
the formulation, discovery and evaluation of scientific hypotheses
the simulation of biological systems at the level of individual molecules

Link @ http://dumontierlab.com/

• ChromHMM software v1.12 (version log)
• ChromHMM manual

Address of the bookmark: http://compbio.mit.edu/ChromHMM/