Results for "C"
Bio-Scripts
Rename the screen name in Linux !
screen -S 22798.pts-5.hn1 -X sessionname node33_COMPUTE766 days ago
Bash online to update Linux OS
sudo bash -c 'for i in update {,full-,dist-}upgrade auto{remove,clean}; do apt-get $i -y; done'751 days ago
- ...assword for neelam: Reading package lists... Done Building dependency tree Reading state i...it. The following additional packages will be installed: li...simulation-tools libgsl23 libgslcblas0 0 upgraded, 3 newly ins...kB/s) Selecting previously unselected pac...
725 days ago
Conda command to install checkV
...V) [jnarayan@hn1 Monkey_Pox]$ conda install -c conda-forge -c bioconda checkv Collecting package metadata (current....68.0 |py36h8619c78_1001 325 KB conda-...6f2f9_0 boost conda-forge/linux-64::boost-1.6...################### | 100% kcounter-0.1.1 | 871 KB...696 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of...m_threads 32 Note: using the -perc_identity flag will speed up t...ity 90 -o -num_threads 32 Next, calculate pairwise ANI by combi...696 days ago
Genome Scaffolding and gap filling !
scaffolding with ARCS v1.0.3 (−c3, −l,4, −a,0.9, −z500, −m50, −20 000, −e30000, −s90). https://github.com/bcgsc/arcs Next, automated gap filling was performed using Sealer v2.0.1 (−L150, -P10, −k75-115 [step = 10]) https://github.com/bcgsc/abyss/tree/sealer-release681 days ago
- (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000
652 days ago
Extract the mapped and unmapped reads !
PROCESSORS=20 #Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapp...End_Layout samtools view --threads $PROCESSORS -b -f 2 in.bam > mapped...651 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; }626 days ago
Identify genome-wide synteny with LASTZ alignment
.... Step1：Mask the repeat sequences for both genomes and chromosomes. RepeatMasker -p...0 -nolow -norna -gff -xmall -lib custom.TE.lib_for_FF.fa FFChr1....in chainPreNet chr01.axt.chain AAChr1.txt.sizes FFChr1.txt.sizes...et.axt.maf Step 3: Get syntenic markers perl Maf2rawsynten...578 days ago
