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Quick next generation sequencing (NGS) terms definition
Last updated 3416 days ago by Neelfragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants,...-
Perl Special Vars Quick Reference
Last updated 3538 days ago by Abhimanyu Singh$_ The default or implicit variable. @_ Subroutine parameters. $a$b sort comparison routine variables. @ARGV The command-line args. Regular Expressions $<digit> Regexp parenthetical capture... -
Source Code and Pseudo Code !!
Last updated 3552 days ago by JitAn algorithm is a procedure for solving a problem in terms of the actions to be executed and the order in which those actions are to be executed. An algorithm is merely the sequence of steps taken to solve a problem. The steps are normally... -
Genome Assembly Tools and Software - PART1 !!
Last updated 3579 days ago by JitThe genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for... -
NGS Glossary !!
Last updated 3762 days ago by Jitalignment: the mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to sequences within the reference genome. Alignment information is stored in the SAM... -
Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass,...
Last updated 3000 days ago by Jitendra NarayanBash Script source: https://gist.github.com/santhilalsubhash/367befcf5216be4b1fd9 Information: This script converts EnsEMBL GTF... -
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
Last updated 3765 days ago by EagleEye----------- Gene Set Clustering based on Functional annotation GeneSCF serves as command line tool for clustering the list of genes given by the users based on functional annotation (Gene Ontology, KEGG, REACTOME and NCG... -
Cheatsheet for Linux !!
Last updated 3767 days ago by JitLinux Commands Cheat Sheet File System ls — list items in current directory ls -l — list items in current directory and show in long format to see perimissions, size, an modification... -
BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data...
Last updated 3607 days ago by JitReformat is a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina... -
Tools for Searching Repeats And Palindromic Sequences
Last updated 3105 days ago by Poonam Mahapatra Comments (2)What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later...
