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• • Jit@jit.aber

  

  Jit bookmarked LibsDyogen: Libibrary for comparative genomics 2363 days ago

  Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications. Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in...

  https://github.com/DyogenIBENS/LibsDyogen
• • Jit@jit.aber

  

  Jit commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2364 days ago

  The Journal of Logic and Computation accept bioinformatics algorithms ans methods papers. https://academic.oup.com/logcom
• • Jit@jit.aber

  

  Jit commented on the blog Tools to detect synteny blocks regions among multiple genomes 2364 days ago

  SynChro seems to be the fastest synteny detection tool. http://www.lcqb.upmc.fr/CHROnicle/SynChro.html https://pdfs.semanticscholar.org/5320/68e328d1aaefa435eefe679f54c018e5c2aa.pdf The paper conclude: SynChro is a fast, efficient and...
• • Jit@jit.aber

  

  Jit answered the question How to fix the following error while compiling MCSCanX ! 2365 days ago

  Follow these steps: (base) ➜  MCScanx git:(master) ✗ for f in msa.h dissect_multiple_alignment.h detect_collinear_tandem_arrays.h ; do sed -i '1 i\#include <unistd.h>' $f ; done(base) ➜  MCScanx git:(master) ✗...
• • Shruti Paniwala@shruti

  

  Shruti Paniwala asked How to fix the following error while compiling MCSCanX ! 2365 days ago

  detect_collinear_tandem_arrays.cc:286:17: note: suggested alternative: 'getpt'     while ((c = getopt(argc, argv, "g:b:c:o:")) != -1)                ...
• • Jit@jit.aber

  

  Jit bookmarked AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome... 2365 days ago

  We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

  https://github.com/CMU-SAFARI/AirLift
• • Jit@jit.aber

  

  Jit bookmarked ‘dockr’: the R container 2365 days ago

  dockr 0.8.6 is now available on CRAN. dockr is a minimal toolkit to build a lightweight Docker container image for your R package, in which the package itself is available. The Docker image seeks to mirror your R session as close as possible with...

  https://www.docker.com/why-docker
• • Neel@neelam

  

  Neel bookmarked SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact... 2366 days ago

  Call sviper ~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants This will output a polished_variants.vcf file, that contains all the refined variants. Sometimes it is helpful to look at the...

  https://github.com/smehringer/SViper
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2368 days ago

  Grep a term from a file in Linux. $ grep -A1 "term" input.fasta > output.fasta #Grep #Term
• • Jit@jit.aber

  

  Jit published a news post 5700 year-old human genome ! 2369 days ago

  Scientists have reconstructed the genome of an ancient human who lived nearly 5,700 years ago in Southern Denmark from the birch pitch- an ancient tar-like substance.
• • Shruti Paniwala@shruti

  

  Shruti Paniwala published a blog post 50 IISC Raman Post Doctoral Fellowships 2369 days ago

  IISC Bangalore has launched Raman Post-Doc Program. Apply For Raman Post Doctoral Fellowship at IISC Bangalore. Bioscience & Chemical Science researchers are eligible to apply for IISC Raman Post Doctoral Fellowships. 50 IISC Raman Post...
• • Jit@jit.aber

  

  Jit bookmarked HaploTypo: a variant-calling pipeline for phased genomes 2369 days ago

  An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve...

  https://github.com/gabaldonlab/haplotypo
• • Jit@jit.aber

  

  Jit posted to the wire 2369 days ago

  The Whole Earth Cataloguer http://www.sactownmag.com/June-July-2018/The-Whole-Earth-Cataloguer/ #Whole #Earth #Cataloguer
• • Shruti Paniwala@shruti

  

  Shruti Paniwala published a blog post Exchange Programme for Indian scientist !! 2370 days ago

  INSA Exchange Programme With Foreign Academies and Organisations
• • Jit@jit.aber

  

  Jit posted to the wire 2370 days ago

  #Bioinformatics #WalkIn at #AIIMS, India https://aiims.edu/images/pdf/recruitment/advertisement/Advertisement%20for%20the%20post%20of%20JRF%20in%20an%20ICMR%20funded%20project.pdf
• • Jit@jit.aber

  

  Jit published a news post BLAST+ 2.10.0 released 2370 days ago

  The BLAST+ 2.10.0 release is now available from at FTP site. The new version offers the following improvements:
• • Rahul Nayak@rahul

  

  Rahul Nayak published a news post ForBio and UiB course: Introduction to phylogenetic methods 2372 days ago

  The is an introductory course that is aimed at students who will need to preform phylogenetic analyses in their work, but who have little or no experience with phylogenetic analyses.
• • Shruti Paniwala@shruti

  

  Shruti Paniwala commented on a bookmark Quick tour of Genetic Algorithms ! 2373 days ago

  Useful links  https://towardsdatascience.com/introduction-to-genetic-algorithms-including-example-code-e396e98d8bf3 https://github.com/memento/GeneticAlgorithm
• • Shruti Paniwala@shruti

  

  Shruti Paniwala created a new bio-script Samtools commands for bioinformatician ! 2373 days ago
• • Jit@jit.aber

  

  Jit bookmarked SeQuiLa-cov: A fast and scalable library for depth of coverage calculations 2373 days ago

  The Docker image is available at https://hub.docker.com/r/biodatageeks/. Supplementary information on benchmarking procedure as well as test data are publicly accessible at the project documentation...

  https://academic.oup.com/gigascience/article/8/8/giz094/5543653

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