Results for "PacBio read correction"
Bio-Scripts
(JitMetaENV) ➜ test_phase_assebly conda install -c bioconda bwise Collecting package...me/urbe/JitSimuStudy/test_phase_assebly directory already exists, BWISE will use it....dy/test_phase_assebly usage: bwise [-h] [-x PAIRED_READFILES]...1043 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 interleav...s/bbmap/current/ align2.RandomReads3 build=1 ref=mixed.fa out=re...3 [build=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interle...len=(0-0) genome=1 PERFECT_READ_RATIO...1042 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta...1029 days ago
Tadpole is 250x faster than SPADes assembler !
...outd= Write discarded reads, if using junk-removal flags. dot...r the primary kmer counts. threads=X Spawn X hashing thread...perform error correction. correct...meo=t (markerrorreadsonly) Only mark bad bases in reads...1029 days ago
Inreractive SCP / File transfer !
#!/bin/bash #next line prints hearer of script echo "Interactive Scrip...value to variable with name desthost read -p "Destination Server Name :...value to variable with name destpath read -p "Destination Path : " dest...value to variable with name filename read -p "P...1003 days ago
- # make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap https...illuminanames=t addslash=t \ pacbio=t pbmin=0.13 pbmax=0.17 \ reads=100 paired=f \ gaussianleng...make 30x haploid coverage for PacBio CLR reads # error rate fro...illuminanames=t addslash=t \ pacbio=t p...
981 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/hifiasm/issues/33 # Use Drosophila melongaster PacBio assembly cd /genetics/elbers...# make reference for randomreads.sh # randomreads.sh part of BBTools/BBMap htt...make 30x haploid coverage for PacBio CLR reads # error rate fro...970 days ago
- $ sudo apt install art-nextgen-simulation-tools [sudo] password for neelam: Reading package lists... Done Building dependency tree Reading state information... Done...y unselected package libgslcblas0:amd64. (Reading da...
717 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; }618 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 genom...478 days ago
