Alignment-free sequence comparison tools available for next-generation sequencing data analysis
kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++)...2365 days ago
2345 days ago
Converting BLAST output into CSV
...ast-to-csv.py using Python: python /root/ngs-scripts/blast/blast-to-csv.py out.txt This outputs a spread-sheet like list of names and e-values. To save this to a file, do:...2331 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hour...2326 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_ .= "\n"'perl -pe 's/$/\n/'perl -nE 'say' # Double space a file...2296 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 frequently used tools for NGS analysis as well as giving experience in writing one-...2275 days ago
Python learning resources for bioinformatics and computational biologist !
Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries. Professionally, P...2249 days ago
Tools to Predict the Impact of Missense Variants !
Prioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A la...2197 days ago
Protein-Protein Interaction Sites Predictions !
The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects...2196 days ago
LINKS scaffolder bloomfilter setting !
➜ 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/u...2145 days ago