Set up WGD environment using conda !
...Verbosity level, default = info. -l, --logfile TEXT File to write logs to (optional) --version Print version number -h, --help...1227 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1020 days ago
Tadpole is 250x faster than SPADes assembler !
...ension. reads=-1 Only process this number of reads, then quit (-1 means...h of that value or lower. prehashes=2 Number of hashes for prefilter. pre...d branches. extendrollback=3 Trim a random number of bases, up to this many, on...1000 days ago
974 days ago
Bash script to simulate a genome !
...asta.gz | \ grep -v ">"|wc -m # 140687135 # 2% heterozygosity is how many bases calc 0.02\*140687135 # 0.02*140687135 = 2813742.700000 # number of mutations added bgzip -@7...941 days ago
918 days ago
Run Pango on your multifasta file !
...a All dependencies satisfied. The query file is:/home/jnarayan/RF_DATA/FASTA/Input_for_Cova_all_samples_combined.fa ** Running sequence QC ** Number of sequences detected: 320 T...911 days ago
Omicron Sequences accession number !
EPI_ISL_6647956 EPI_ISL_6647957 EPI_ISL_6647958 EPI_ISL_6647959 EPI_ISL_6647960 EPI_ISL_6647962 EPI_ISL_6647961 Search the IDs in https://www.epicov.org/epi3/frontend909 days ago
Extract all fasta sequences except ids !
...n=omi_kmer19.fa out=omi_kmer19_formated.fa fastawrap=19 #Extract and number the kmers perl storeKmer.pl omi_kmer19_formated.fa > omi_kmer19_formated_numbered.fa # cat all *.rd file...852 days ago
Count number of lines in each file in Linux !
for FILE in *.rd; do wc -l $FILE; done > allReads.hits830 days ago