Type-Nannopore

⬝Merge samples ➔ Filter ➔Down samples

⬝Merge options: ➔Filter options:

Min quality: 10 (?)
Min read length: 200 (?)
Max read length: 5000 (?)
Extra ends trim: 20 (?)

➔Down sample options:

Max number of reads: 10000 (?)

➔Upload samples➔ Merge➔ change name➔ Save ➔New analysis:

Met on time
Kraken 2

Met on time:

Database sequence: choose data same database taxonomy
Database taxonomy: choose data same database sequence

NOTE: Database sequence and database taxonomy have to select the same file.The blank box "select a database sequence/taxonomy" is a file available in the software, while the "choose file" section can select files in the program.

Number of threads (number of CPU cores you want to run in the machine): Not too big and not too small, normal machines are around 15-16, better machines are around 30-32
Max accepts (number of reads accepted): usually 1
Minimum query coverage (percentage add read): Minimum query coverage should be small value
Minimum identity threshold (comparison threshold acceptance rate): Minimum query coverage should be small value

⬝Export unassigned read: create a fasta file containing sequents not found in the data base

⬝Classifier: Vsearch is a software tool in the field of digital biology, used mainly for data analysis applications. It is designed to perform tasks such as clustering, classification, string search, and others related to genomic and metagenomic data processing and analysis. Some of the main functions of VSEARCH include:
- Clustering: Grouping reads or strings based on similarity.
- Classification: Identification of genomic or metagenomic sequences belonging to taxonomic groups.
- Search: Search for strings that are highly similar to a reference string. Poor quality removal: Removes reading passages or strings that are of poor quality.
BLAST: is a software tool used in the field of molecular biology and computational biology. It is designed to search for similar nucleotide sequences or proteins in known sequence databases. BLAST allows users to compare a query to one or more databases and find similar objects in that database such as:

⬝Comparing nucleotide sequences with a database of nucleotide sequences.

⬝Comparing protein sequences with a database of protein sequences.

⬝Comparing nucleotide sequences with a database of protein sequences.

⬝Comparing protein sequences with a database of nucleotide sequences.

⬝Comparing nucleotide sequences with a database of nucleotide sequences in duplicate pairs of 6-frame translation.

BLAST ➔edit ➔export ➔evaluate

Kraken 2: is a bioinformatics tool used for metagenomic sequence classification. It is designed to rapidly and accurately classify DNA sequences obtained from metagenomic samples. Kraken 2 is based on the concept of k-mer matching, where short subsequences of DNA (k-mers) are compared against a reference database of genomes or sequences to determine their taxonomic origin.