Results for "AP"
Bio-Scripts
...➜ test_phase_assebly bwise *** This is BWISE - High order De Bruijn graph assembler *** The command...-p SR_SOLIDITY] [-P SR_COVERAGE] [-k K_MIN] [-K K_MAX] [-e MAPPING_EFFORT] [-a...1048 days ago
Commandline for paired end reads simulation with BBMap !
...t:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved read...62129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3...=1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interleaved, r...t size=400-600 Wrote reads_BBMAP250.fq Time: 5.722 seconds.1048 days ago
List of string comparison algorithms !
String comparison: Levenshtein Distance Damerau-Levenshtein Distance Jaro Distance Jaro-Winkler Distance Match Rating Approach Comparison Hamming Distance More at https://jellyfish.readthedocs.io/en/latest/comparison.html1040 days ago
- Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/$ sudo apt install jellyfish Reading package lists... Done Building depen....15.0-147-generic linux-modules-extra-4.15.0-151-generic Use 'sudo apt autoremove' to remove them....
1039 days ago
Print in terminal with python !
#!/usr/bin/env python import time import curses def pbar(window): height, width = window.getmaxyx() for i in range(10): window.addstr(height -1, 0, "[" + ("=" * i) + ">" + (" " * (10 - i )) + "]") window.refresh() time.sleep(0.5) curses.wrapper(pbar)1036 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyToo...m 63-93, etc. Please read bbmap/docs/guides/TadpoleGuide.txt...rite a contigs connectivity graph (partially implemented) dum...ore the contig connectivity graph. (partially implemented)...Controls whether a path appears to be continuous. paths...1034 days ago
Trim the reads in loop using Trimmomatic !
...rim.fastq.gz \ ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz \ SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 done1013 days ago
Perl script for Smith-Waterman Algorithm
...= @ARGV; # scoring scheme my $MATCH = 1; # +1 for letters that match my $MISMATCH = -1; # -1 for letters that mismatch my $GAP = -1; # -1 for any gap # initialization my @matr...1008 days ago
- ...2-pass [Integer] default = 0 -F Filter query sequence with SEG [String] default = F -G Cost to open a gap [Integer] default = 11 -E Cost to extend a gap [Integer] default = 1...
1008 days ago
Get the Linux system information !
...driven system information program DIALOG_CANCEL=1 DIALOG_ESC=255 HEIGHT=0 WIDTH=0 display_result() { dialog --title "$1" \ --no-collapse \ --msgbox "$result" 0...1006 days ago
