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Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
Last updated 2480 days ago by Rahul NayakThe 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-liners. File System ls — list items in current directory ls...-
List of visualization tools for genome alignments
Last updated 2484 days ago by Rahul NayakGenome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which... -
Comprehensive list of visualization tools for biological pathways
Last updated 2487 days ago by NeelThe study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads... -
List of visualization tools for network biology
Last updated 2488 days ago by JitNetwork analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which... -
sam to bam conversion !!
Last updated 2491 days ago by JitTo do sam to bam conversion, follow the following commands :- Code: $ samtools view -b -S file.sam > file.bam Then you will need to use Code: $ samtools sort file.bam file-sorted followed by Code: $ samtools index... -
PerlOneLiner for Bioinformatician
Last updated 2502 days ago by Shruti PaniwalaFILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_ .= "\n"'perl -pe 's/$/\n/'perl -nE 'say' # Double space a file, except the blank linesperl -pe '$_ .= "\n" unless /^$/'perl -pe '$_ .= "\n" if... -
Converting FASTQ to FASTA
Last updated 2505 days ago by NeelThere are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the... -
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
Last updated 2514 days ago by Poonam Mahapatra Comments (1)BBSplit internally uses BBMap to map reads to multiple genomes at once, and determine which genome they match best. This is different than with ordinary mapping. If a genome (say, human) contains an exact repeat somewhere, reads mapping to it will... -
Bioinformatics Web Application Development with Perl
Last updated 2521 days ago by JitPerl's second wave of adoption came from the growth of the world wide web. Dynamic web pages—the precursor to modern web applications—were easy to create with Perl and CGI. Thanks to Perl's ubiquity as a language for system... -
Run miniasm assembler on nanopore reads !
Last updated 2530 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
