Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1340 days ago
1260 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LWP::Simple; use Archive::Extract; # # First, check if all the required modules have been installed in the...1217 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my_file do filename=$(basename "$my_file") basenam...1101 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1052 days ago
Python script to read FASTA and FASTQ file !
...rt FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam.FastxFile`. Args: fasta_q_file (str): Path to FASTA/Q file. """ with F...1033 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh Written by Brian Bushnell Last modified July 16, 2018 Description: Uses kmer counts to as...1032 days ago
1006 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' program is available in the legacy NCBI BLAST...1006 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name Type Taxonomy Url - UniRef100 Aminoacid yes https://www.unipr...998 days ago