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1576 days ago
Perl one-liner for beginners !
I often use the following arguments to perl: -e Makes the line of code be executed instead of a script -n For...1409 days ago
Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assem...anup of read files.This function trims adapters, barcodes and other contaminants from...ioinf.spbau.ru/quastMauve assembly metrics - http://code.google.com/p/ngopt/wiki/How_T...1232 days ago
Run bash script in Perl program !
BioPerl is a compilation of Perl modules that can be used to build bioinformatics-related Perl scripts. It is used, for example, in the development of source codes, standalone software/tools,...665 days ago
Levenshtein and Damerau-Levenshtein distance !
Levenshtein Distance Also known as Edit Distance, it is the number of transformations....Edit Distance is very easy to implement, and it is a popular challenge during code interviews Additionally, so...978 days ago
Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake &ldq...962 days ago
Classification of SARS-CoV2 Variant !
The scientists established some guidelines for determining whether a variant is a legi...iffer from its ancestor by at least one nucleotide.At least 95% of its genetic code should have been sequenced at...919 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignme...905 days ago
Understanding DUMP files from NCBI Taxonomy database !
*.dmp files are bcp-like dump from GenBank ta...dom, kingdom, ...) embl code -- locus-name prefix; not uni...division from parent genetic code id -- see gencode.dmp file &...id division cde -- GenBank division code (three characters) division...688 days ago