BOL

BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and...

Research funding in India https://www.ncbs.res.in/rdo/sponsor-grants #India #Funding

I like python for following regions :  1. Easy Syntax: Python Syntax are easy to learn and implement by Both Non-Programmers as well as an Experienced Programmer. 2. Readability:  Python Syntax are Clear to read since each...

WalkIn for Bioinformatics at CIFRI http://www.cifri.res.in/wknintrwv1.pdf #CIFRI #WalkIn

Understanding HGT https://www.youtube.com/watch?v=ivxnXZQ7_xY #HGT #Gene #Video

fragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants,...

tardis Toolkit for Automated and Rapid DIscovery of Structural variants Requirements zlib (http://www.zlib.net)mrfast (https://github.com/BilkentCompGen/mrfast)htslib (included as submodule; http://htslib.org/)Fetching tardis git clone...

Method journals also published bioinformatics research papers http://www.sciencedirect.com/science/journal/10462023

The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

Convert masked genome to N letters. $ perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna #Genome #Masked #N #Convert

Unmasking the lower case values in genome. $ perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #Genome #Unmask #Perl #Oneliner

Update CPAN $ cpan> install CPAN; reload cpan #cpan #perl

Bedtools wiki https://code.google.com/archive/p/bedtools/wikis/Usage.wiki #Wiki #Bedtools

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.htmlFeatures    Mapping position agnostic to alignment parameters.   ...

Handling #CSV file with #Perl http://perlmeme.org/tutorials/parsing_csv.html

Following are the list of Springer bioinformatics journals https://link.springer.com/search?query=bioinformatics&facet-content-type=%22Journal%22