2872 days ago
Genome Assembly Tools and Software - PART1 !!
...1], which can assemble select regions surrounding interesting featu...ative data, analyzing the gap region and indicating the best seque...s each graph independently to extract full-length splicing isoform...access and navigation to any region of interest, and whole contig...2689 days ago
Quick next generation sequencing (NGS) terms definition
fragment size: the Illumina WGS protocol generates pa...gt;90%) of paired-end reads are sampled from no-SV regions, therefore the fragment size...read depth: number of reads that map within a region of the genome. Overall genome...2526 days ago
Awesome perl frameworks, libraries and software - PART 1
A curated list of awesome Perl frameworks, libraries and software. major/MySQLTuner-perl - MySQLTuner is a s...loyed mod_perl application on the planet. mharsch/arcstat - uses Perl to extrac...2493 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\...ers by one in the string$str =~ s/(\d+)/$1+1/ge # Extract HTTP User-Agent string from t...>$html =~ s|<(/)?b>|<$1strong>|g # Extrac...2306 days ago
Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
The purpose of this cheat sheet is to introduce biologist and bioinformatician to the fr....tar containing files tar xf file.tar — extract the files from file.tar tar c...Gzip compression tar xzf file.tar.gz — extrac...2284 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumina...he contigs you have identified as overlapping your region of interest, and the set S of...3. If you don't have a complete assembly of the region of interest, generate an STS...2168 days ago
My commonly used commands in Bioinformatics
FYI, 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....2114 days ago
Steps to find all the repeats in the genome !
To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--...nerate several output files, including a .out file. You can parse this file to extrac...252 days ago