Indexed reference databases for KMA and CCMetagen

Abstract

This database was built to identify taxa in metagenome samples using the CCMetagen pipeline. The whole NCBI nt collection allows a complete taxonomic overview, including from microbial eukaryotes that may be present in the dataset. This database is already indexed, ready to use with KMA and CCMetagen. A manual describing how to use this dataset can be found at: https://github.com/vrmarcelino/CCMetagen Additionally, a tutorial on the whole analysis of a set of metatranscriptome samples can be found at: https://github.com/vrmarcelino/CCMetagen/tree/master/tutorial The database was built as follows: The partially non-redundant nucleotide database was downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz) in January 2018. This database was formatted to include taxids in sequence headers. Indexing was then performed with KMA using the commands: kma_index -i nt_taxid.fas -o ncbi_nt -NI -Sparse TG Three indexed databases are provided: 1 - NCBI nucleotide collection 2 - RefSeq database of bacterial and fungal genomes. V 1.0 - Initial Upload. V 2.0 - Addition of NCBI database: The NCBI nucleotide collection contains many environmental and artificial sequence entries without taxonomic information (e.g. uncultured marine bacteria). We therefore compiled a database without those. The file ncbi_nt_no_env_11jun2019.zip contains therefore all ncbi nt entries excluding the descendants of environmental eukaryotes (taxid 61964), environmental prokaryotes (48479), unclassified sequences (12908) and artificial sequences (28384).