3979 days ago
Most Commonly used Awk by Bioinformatician
...cover most of bioinformatician daily uses of awk. choose rows where column 3 is larger than column 5: awk '$3>$5' input.txt > output.txt extract column 2,4,5: awk '{print $2...3944 days ago
List of In-silico Binding Site Prediction Tools
...a binding ligand(s). Essentially, we use a purely geometric method to extract site-specific spatial pattern...includes two other programs (dpocket & tpocket) that allow you to extract pocket descriptors and test o...3776 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...whole genome sequencing data” Input: depth file generated by DFExtract and a config file Output: .r...ption of flat tabular format VariantMaster Description: “extract causative variants for monoge...2940 days ago
2906 days ago
Genome Assembly Tools and Software - PART1 !!
...al de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms...2717 days ago
Awesome perl frameworks, libraries and software - PART 1
...anagement system and web application framework. The most widely deployed mod_perl application on the planet. mharsch/arcstat - uses Perl to extract, format, and display kstats f...2521 days ago
PerlOneLiner for Bioinformatician
...# Increase all numbers by one in the string$str =~ s/(\d+)/$1+1/ge # Extract HTTP User-Agent string from t...tags with <strong>$html =~ s|<(/)?b>|<$1strong>|g # Extract all matches from a regular ex...2334 days ago
Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
...ate a tar named file.tar containing files tar xf file.tar — extract the files from file.tar tar c...h; create a tar with Gzip compression tar xzf file.tar.gz — extract a tar using Gzip gzip file&nb...2312 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.gz | raco...2142 days ago