BOL

Thanks for reporting the updated tool for assembly validation, you can also try following methods/pipelines

• CEGMA (formally discontinued but still useful)
• BUSCO (we have issues with fish, seems not to be tailored to that group of organisms, developers tell us they are fixing it)
• linkage map? or other map (RAD-tag based). (software?)
• BioNanoGenomics can be used for QC also
• Use a genome browser to get a feeling for your results, e.g. IGV; add assembly, BAM files, annotation, transcripts mapped and browse

How can I generate a Venn diagram in R? by UCLA is also useful http://www.ats.ucla.edu/stat/r/faq/venn.htm

Six-way Venn diagram

https://stackoverflow.com/questions/32440128/nice-looking-five-sets-venn-diagrams

Bioinformatics funding for Japan

Promoting science and technology is a key engine to materialize a bright future of Asia and it is vitally important to enhance the exchange of youths in Asian countries and Japan who will play a crucial role in the field of science and technology.

Based on this concept, “Japan-Asia Youth Exchange Program in Science” (SAKURA Exchange Program in Science) is the program for enhancing exchanges between Asia and Japan of the youths who will play a crucial role in the future field of science and technology through the close collaboration of industry-academia-government by facilitating short-term visits of competent Asian youths to Japan. This program aims at raising the interest of Asian youths toward the leading Japanese science and technologies at Japanese universities, research institutions and private companies.

More at http://www.ssp.jst.go.jp/EN/outline/index.html

The Arturo Falaschi ICGEB Fellowship Programmes for PhD, PostDoc and Short term courses

The Arturo Falaschi ICGEB Fellowships programme offers long and short-term fellowships for scientists who are nationals of ICGEB Member States to perform research in Trieste, New Delhi or Cape Town.

More at http://www.icgeb.org/fellowships.html

Try this https://www.birac.nic.in/big.php if you dream ur company

https://www.uniraj.ac.in/uic/

Common usage 

SPAdes: de Bruijn graph based assembler

The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final assembly from multiple kmers. A list of kmers is automatically selected by SPAdes using the maximum read length of the input data, and each individual kmer contributes to the final assembly. To run SPAdes we will use the spades.py command with the --careful option to minimize the number of mismatches in the contigs, -o for the output folder, -1 for the path to the forward reads, -2 for the path to the reverse reads, and -s for the path to the singles reads. If desired, a list of kmers can be specified with the -k flag which will override automatic kmer selection.

spades.py --careful -o SPAdes_out -1 /common/Assembly_Tutorial/Quality_Control/Sample_1.fastq -2 /common/Assembly_Tutorial/Quality_Control/Sample_2.fastq -s /common/Assembly_Tutorial/Quality_Control/Sample_s.fastq

The latest relase of LastZ at http://www.bx.psu.edu/~rsharris/lastz/newer/

Understanding lastz http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf