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BioStar on Keep Your Important SSH Session Running when You Disconnect from Server !!! (136 days ago): To block a node srun --partition=compute --nodes=1...- BioStar on Benchmarking Perl Module ! (615 days ago): Benchmarking a Perl module involves measuring the performance of the module in...
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Bioinformatics Training Courses At RASA LSI
Last updated 1842 days ago by RASA Life SciencesRASA conducts comprehensive Life Science skill development training courses in Pune, India for working professionals, researchers, students and job-seeker. The trainings are crafted meticulously, covering different modules of courses such as...-
Installing BLAT on Linux !
Last updated 2263 days ago by BioStar Comments (1)It's been a while since I last installed BLAT and when I went to the download directory at UCSC: http://users.soe.ucsc.edu/~kent/src/ I found that the latest blast is now version 35 and that the code to download was: blatSrc35.zip.... -
Benchmarking Perl Module !
Last updated 2280 days ago by Rahul Nayak Comments (1)The benchmark module is a great tool to know the time the code takes to run. The output is usually in terms of CPU time. This module provides us with a way to optimize our code. With the advent of petascale computing and other multicore processor it... -
Parallel Processing with Perl !
Last updated 2280 days ago by Rahul NayakHere is a small tutorial on how to make best use of multiple processors for bioinformatics analysis. One best way is using perl threads and forks. Knowing how these threads and forks work is very important before implementing them. Getting to know... -
List of non-commercial NGS genotype-calling software
Last updated 2296 days ago by Jit Comments (1)Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and... -
My commonly used commands in Bioinformatics
Last updated 2310 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta... -
Interview Puzzles for Bioinformatician !
Last updated 2319 days ago by Rahul Nayak Comments (1)These are some of the most famous Interview Puzzles being asked in top tech companies.Here is a list of Top 25 puzzles which have been asked in top Tech Interview. 2 Eggs and 100 Floor Classic Puzzle Five pirates and gold coin Puzzle Six... -
Understanding BLASTn output format 6 !
Last updated 2338 days ago by Rahul NayakBLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident... -
LINKS scaffolder bloomfilter setting !
Last updated 2351 days ago by Jit➜ bin git:(master) ✗ ls -l total 68 drwxrwxr-x 3 urbe urbe 4096 Jun 15 12:15 lib -rwxrwxrwx 1 urbe urbe 65141 Jun 15 17:13 LINKS ➜ bin git:(master) ✗ pwd /home/urbe/Tools/LINKS_1.8.6/bin ➜ bloomfilter git:(master) ✗ swig -Wall -c++... -
Gap filling or Contigs extensions tools !
Last updated 2365 days ago by Rahul NayakThere are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within paired reads" or "Toward almost closed genomes with GapFiller". There are also some tools like...
