Results for "C"
Bio-Scripts
Commandline for paired end reads simulation with BBMap !
...axinsert=600 gaussian java -ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3 bu..., maxinsert=600, gaussian] Writing reference. Executing dna.FastaToChrom...Rate =0.0, max=0, len=(0-0) genome=1 PERFECT_READ_RATIO=0.0 ADD_ERRORS_F...1048 days ago
Commands to transfer files and folder in docker !
#To copy files between host machine and container (execute the commands on host, not inside container): $ docker cp FILE_OR_FOLDER_ON_HOST CONTAINER_ID:/CONTAINER_DIRECTORY #or $ docker cp CONTAINER_ID:FILE_OR_FOLDER_IN_CONTAINER HOST_DIRECTORY1044 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
- ...install jellyfish Reading package lists... Done Building dependency tree Reading state i...linux-headers-4.15.0-144-generic linux-headers-4.15.0-147 linu...linux-modules-4.15.0-144-generic linux-modules-4.15.0-147-gene...n, 808 kB of additional disk space will be used. Do you want t...
1040 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
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def r...asta_q_file) as fh: for entry in fh: sequence_id = entry.name sequence = entry.sequence1035 days ago
Remove dupcates in multifasta file !
#Using seqkit for duplicate sequence removal seqkit rmdup -n seqs.fa -o seqs_without_duplicate.fa #Awk for duplicate sequence removal awk '/^>/ { f = !a[$0]++ } f' seqs.fa1034 days ago
Tadpole is 250x faster than SPADes assembler !
...modified July 16, 2018 Description: Uses kmer counts to assemble contigs, ext...as kmer counts. Much faster but counts...izes. discard: Discard low-depth reads,...testmerge=t Test kmer counts around the read merge ju...1034 days ago
- # Make sure that Java v8+ is installed: java -version # Install Nextflow curl -fsSL get.nextflow.io | bash # Add Nextflow binary to your PATH: mv nextflow ~/bin/ # OR system-wide installation: # sudo mv nextflow /usr/local/bin
1021 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D1020 days ago
