BBTools for bioinformatician !
...ta file containing the sequence between the primers, for each reference sequence. We used these programs to synthetically cut V4 out of full-length 16S sequences.I should say, thoug...2269 days ago
10 days ago
Barrnap: Bacterial ribosomal RNA predictor
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes F...2548 days ago
2865 days ago
Genome Assembly Tools and Software - PART1 !!
...pore flow cell technologies (MinION). REAGO 1.1 – REconstruct 16S ribosomal RNA Genes from MetagenOmic data an assembly tool for 16S ribosomal RNA recovery from m...2684 days ago
Frequent parameters for bioinformatics tools !
...p; MeDuSa -random 100 Prokka --usegenus --force --addgenes --rfam --rawproduct cmsearch (taxonomy, 16S) --rfam --noali blastn (taxonomy, 16S) -evalue 1E-10 blas...1284 days ago
Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
...o quickly identify source organisms. The new databases are: *16S ribosomal RNA (Bacteria and A...1532 days ago
Senior Scientist bioinformatics @ Eurofins Genomics India Pvt Ltd, Bengaluru.
...data -Organizing and managing large scale genomic data -Should have experience in NGS data analysis, such as WGS, RNASeq, Small RNA, Metagenome (16S, ITS, Whole metagenome)etc....993 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...aDB #https://www.arb-silva.de/no_cache/download/archive/release_138_1/Exports/ #LSU: Large subunit (23S/28S ribosomal RNAs) #SSU: Small subunit (16S/18S ribosomal RNAs) my $si...1159 days ago
Installing Covid19 Environment !
...rona/taxonomy ktUpdateTaxonomy.sh \ The default QUAST package does not include: * GRIDSS (needed for structural variants detection) * SILVA 16S rRNA database (needed for ref...922 days ago
Barrnap: Bacterial ribosomal RNA predictor
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMME...Tags: Bioinformatics, RNA, Barrnap, 5S, 23S, 16S
2548 days ago
Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism
MCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples. To provide easy access to these sequences, ...Tags: Curated, ribosomal, RNA, rRNA, reference, sequences, targeted, loci, verifiable, organism, 16S, 18S, 28S, ribosomal, RNA
1532 days ago
Comment on "Setting up autoConTAMPR !"
...(This frontend requires a controlling tty.)debconf: falling back to frontend: Teletypedpkg-preconfigure: unable to re-open stdin: Fetched 365 kB in 16s (21.5 kB/s)Selecting previous...1440 days ago