Results for "PE"
Bio-Scripts
...cation: /home/me/anaconda3 added / updated specs: - conda The foll...e REMOVED: entrez-direct-15.6-he881be0_1 perl-archive-tar-2.32-pl526_0...pl526hc9558a2_0 perl-exporter-5.72-pl526_1 perl-exporter-tiny-1.002001-pl52...847 days ago
Command line to move all files from a directory !
find ~/Downloads/ -type f -print0 | xargs -0 mv -t ~/Videos780 days ago
- ...[sudo] password for neelam: Reading package lists... Done Building dependency tree Reading st...emove and 1 not upgraded. Need to get 2,616 kB of archives. After this operation, 12.3 MB of additional...
727 days ago
Conda command to install checkV
.../man/anaconda3/envs/jitENV added / updated specs: - checkv The fol...pyhd8ed1ab_0 44 KB conda-forge openssl-1.1.1q |...2-h166bdaf_2 The following packages will be SUPERSEDED by a higher-priority ch...698 days ago
Script to rapid genome clustering based on pairwise ANI
...blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of seq...o -num_threads 32 Note: using the -perc_identity flag will speed up...pairs: anicalc.py -i -o Finally, perform UCLUST-like clustering u...697 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-release682 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
654 days ago
Extract the mapped and unmapped reads !
...s view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam #Paired_End_Layout s...view --threads $PROCESSORS -b -F 2 in.bam > unmapped.bam652 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; }628 days ago
Identify genome-wide synteny with LASTZ alignment
...nteny markers based on LASTZ alignment. Step1：Mask the repeat sequences for both genomes and chromosomes. RepeatMasker -pa 40 -nolow -norna...lter.tnet.synnet.axt.maf Step 3: Get syntenic markers perl Maf2rawsynteny.pl chr1.chai...579 days ago
