MATEdb: Metazoan Assemblies from Transcriptomic Ensembles

This release contains 9 tar.gz folders. Each of them contains two folders, Arthropoda and Mollusca which in turn contain the files for the species that belong to each phyla. <br> <strong>MATEdb_trinity_assemblies.tar.gz</strong> Contains the assembled transcriptomes. The raw data was downloaded from the Sequence Read Archive (SRA) from NCBI using the SRA Toolkit version 2.10.7 whenever possible or manually from other repositories. Next, the raw data was filtered using fastp version 0.20.1. Finally it was assembled using Trinity version 2.11.0. <br> <strong>MATEdb_transdecoder_cds.tar.gz</strong> Contains the ORFs, in nucleotides, for all transcripts annotated using TransDecoder 5.5.0. The TransDecoder.LongOrfs was run to extract all ORFs with a minimum length of 100 amino acids. Next TransDecoder.Predict was run training with the top 25% longest ORFs. <br> <strong>MATEdb_transdecoder_pep.tar.gz</strong> Same as MATEdb_transdecoder_pep.tar.gz but the sequences are in amino acids. <br> <strong>MATEdb_blobtools_filtered_cds.tar.gz</strong> Contains the files from MATEdb_transdecoder_cds filtered by removing the transcripts with a non-metazoan origin using BlobTools v2.3.3. The files in MATEdb_blobtools_filtered_pep were mapped against the nr (non-redundant protein) database using diamond blastp version 2.0.8. This file was used to create a database, using the create command from BlobTools, which was used to obtain the list of contaminants using the extract_phyla_for_blobtools.py custom script. Next the filter command from BlobTools was used to remove non-metazoan transcripts. <br> <strong>MATEdb_blobtools_filtered_pep.tar.gz</strong> Same as MATEdb_blobtools_filtered_cds.tar.gz but the sequences are in amino acids. <br> <strong>MATEdb_longest_pep.tar.gz</strong> Contains the files that include only the longest isoform for each gene in amino acids. These were obtained using the custom script fetch_longest_iso.py <br> <strong>MATEdb_genomes_cds.tar.gz</strong> Contains the sequences in nucleotides corresponding to the longest isoform for every coding gene. The sequences were downloaded from different sources for each species and the longest isoform was obtained using the custom script fetch_longest_iso.py <br> <strong>MATEdb_genomes_pep.tar.gz</strong> Same as MATEdb_genomes_cds.tar.gz but the sequences are in amino acids. <br> <strong>MATEdb_eggnog_annotation.tar.gz</strong> Contains the eggnog annotation for the longest isoform for every species in the database. EggNOG-mapper version 2.1.6 was used. <br> For more details see: https://github.com/MetazoaPhylogenomicsLab/MATEdb