Results for "5"
Bio-Scripts
Install trimmomatic using Conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioco...ersion of conda exists. pkgs/main::certifi-2021.5.30-py37h06a4308_0 Procee...ownloading and Extracting Packages certifi-2021.5.30 | 139 KB | #########...1117 days ago
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1117 days ago
- ...| py37h06a4308_11 25 KB jellyfish-2.2.10...393 KB bioconda jemalloc-4.5.0 |...bioconda/linux-64::jemalloc-4.5.0-0 kat bio...## | 100% kat-2.0.8 | 7.5 MB | #####################...
1109 days ago
- ...d ---------------------------|----------------- jemalloc-5.2.1 | h2531618_5 1.0 MB od...UPDATED: jemalloc bioconda::jemalloc-4.5.0-0 --> pkgs/main::jemalloc-5...
1109 days ago
- ...nda btrim-1.0.1 | h7d875b9_3 48 KB bioconda...b76_1 11 KB bioconda certifi-2021.5.30 | py36h5fab9bb_...08_1 certifi 2020.12.5-py36h5fab9bb_1 --> 2021.5.30-...
1053 days ago
Commandline for paired end reads simulation with BBMap !
...ndomreads.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250 mininsert=400 maxinsert=600...ads3 build=1 ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=...in, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, mi...1053 days ago
- Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/$ sudo apt...nger required: linux-headers-4.15.0-144 linux-headers-4.15.0-144-generic linux-headers-4....15.0-147-generic linux-modules-4.15.0-151-generic linux-modules-e...64 jellyfish amd64 2.2.8-3build1 [358 kB] Fetched 418 kB in 1s (4...
1044 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)1041 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole....specified; default is 1. minprob=0.5 Ignore kmers with ove...der this. pathsimilarityfraction=0.45(psf) Max difference ratio con...ify 200 megs. The max is typically 85% of physical memory. -eoom...1039 days ago
Trim the reads in loop using Trimmomatic !
...n.trim.fastq.gz \ ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz \ SLIDINGWINDOW:4:20 MINLEN:25 ILLUMINACLIP:NexteraPE-PE.fa:2:40:15 done1018 days ago
