1005 days ago
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt1005 days ago
999 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400...999 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam.F...985 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 ass...985 days ago
Inreractive SCP / File transfer !
#!/bin/bash #next line prints hearer of script echo "Interactive Script to Copy File (files) / Directory using scp" #next line check if entered value is not null, and...959 days ago
673 days ago
Perl script to read the next line of a file !
my $line = ; while(1) { # keep looping until I say so my $nextLine = ; if ($line =~ m/>/ || !defined $nextLine) { ### Do the stuff } ### Do any other stuff; last unless defined $nextLine; $line = $nextLine; }574 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $...434 days ago