bpbowen/SynCom17_EcoFab

Sequence Data for the 17 member SynCom

Described in "Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems"

• https://www.biorxiv.org/content/10.1101/2024.10.02.615924v1
• doi: https://doi.org/10.1101/2024.10.02.615924

The genomic DNA was submitted to the Joint Genome Institute for sequencing using PacBio Sequel II or Illumina NovaSeq S4. Genomes were stored in the Genomes OnLine Database (GOLD), followed by submission to the Integrated Microbial Genomes and Microbiomes (IMG/M) (https://img.jgi.doe.gov/) for annotation.

Inside 17_member_syncom_IMG-GOLD_metadata.tsv

['taxon_oid', 'taxon_display_name', 'domain', 'phylum', 'ir_class',
       'ir_order', 'family', 'genus', 'species', 'seq_status', 'seq_center',
       'analysis_project_id', 'ncbi_taxon_id', 'is_public', 'add_date']

Inside each .tar.gz bundle file:

<taxon_oid>.fna - FASTA nucleic acid file for taxon.
<taxon_oid>.genes.fna - FASTA nucleic acid file for genes.
<taxon_oid>.genes.faa - FASTA amnio acid file for genes.
<taxon_oid>.intergenic.fna - FASTA for intergenic regions.
<taxon_oid>.gff - Tab delimited in mostly GFF3 format for genes.
  (Strict conformance is not guarantted, esp. in type and attributes fields.)
<taxon_oid>.cog.tab.txt - Tab delimited file for COG annotation.
<taxon_oid>.kog.tab.txt - Tab delimited file for KOG annotation.
<taxon_oid>.pfam.tab.txt - Tab delimited file for Pfam annotation.
<taxon_oid>.tigrfam.tab.txt - Tab delimited file for TIGRFAM annotation.
<taxon_oid>.ipr.tab.txt - 
  Tab delimited file for "other" (Non-Pfam/TIGRFAM) InterPro hits.
  (Optional)
<taxon_oid>.ko.txt - Tab delimited file for KO and EC annotation.
<taxon_oid>.signalp.txt - Tab delimited file for signal peptide annotation.
<taxon_oid>.tmhmm.txt - Tab delimited file for transmembrane helices.
<taxon_oid>.xref.tab.txt - Tab delimited file for external references.
     (Data is spotty and optional.)
<taxon_oid>.crispr.txt - Tab delimited file for CRISPR details.

(For some of the smaller genomes, e.g., viruses, not all annotation files is present. If the genome has no annotation of a certain type, e.g. no TIGRFAM's, the annotation file .tigrmfam.tab.txt is not there. Some annotations are not done at all, e.g. InterPro for metagenomes. Any file that does not have annotations or has no data will not be present.)

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Structure of each tab delimited file:

<taxon_oid>.gff
-- seqid - Sequence ID
-- source - version of IMG database
-- type - feature type
-- start_coord - starting coordinate
-- end_coord - ending coordinate
-- score - NA
-- strand
-- phase - NA
-- attributes - ID=<gene_oid>;locus_tag=<locus_tag>;product=<product name>

<taxon_oid>.cog.tab.txt (from NCBI RPSBLAST)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- percent_identity - Perceent identity of aligned amino acid residues
-- query_start - Start coordinate of alignment on query gene
-- query_end - End coordinate of alignment on query gene
-- subj_start - Start coordinate of alignment on subject sequence
-- subj_end - End coordinate of alignment on subject sequence
-- evalue - Expectation value
-- bit_score - Bit score of alignment
-- cog_id - COG identifier
-- cog_name - COG name
-- cog_length - Length of COG consensus sequence

<taxon_oid>.kog.tab.txt (from NCBI RPSBLAST)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- percent_identity - Perceent identity of aligned amino acid residues
-- query_start - Start coordinate of alignment on query gene
-- query_end - End coordinate of alignment on query gene
-- subj_start - Start coordinate of alignment on subject sequence
-- subj_end - End coordinate of alignment on subject sequence
-- evalue - Expectation value
-- bit_score - Bit score of alignment
-- kog_id - KOG identifier
-- kog_name - KOG name
-- kog_length - Length of KOG consensus sequence

<taxon_oid>.pfam.tab.txt (from EBI's pfam_scan which uses HMMER 3.0)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- query_start - Start coordinate of alignment on query gene
-- query_end - End coordinate of alignment on query gene
-- subj_start - Start coordinate of alignment on subject sequence
-- subj_end - End coordinate of alignment on subject sequence
-- evalue - Expectation value
-- bit_score - Bit score of alignment
-- pfam_id - Pfam identifier
-- pfam_name - Pfam name
-- pfam_length - Length of Pfam consensus sequence

<taxon_oid>.tigrfam.tab.txt (from hmmscan HMMER3.0)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- query_start - Start coordinate of alignment on query gene
-- query_end - End coordinate of alignment on query gene
-- evalue - Expectation value
-- bit_score - Bit score of alignment
-- tigrfam_id - TIGRFAM identifier
-- tigrfam_name - TIGRFAM name

<taxon_oid>.ipr.tab.txt 
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- query_start - Start coordinate of alignment on query gene
-- query_end - End coordinate of alignment on query gene
-- domaindb - Original domain database.
-- domainid - ID on original domain database.
-- iprid - InterPro ID.
-- iprdesc - InterPro description.
-- go_info - Gene Ontology Information

<taxon_oid>.ko.tab.txt (from NCBI BLASTP on KEGG genes)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- percent_identity - Perceent identity of aligned amino acid residues
-- query_start - Start coordinate of alignment on query gene
-- query_end - End coordinate of alignment on query gene
-- subj_start - Start coordinate of alignment on subject sequence
-- subj_end - End coordinate of alignment on subject sequence
-- evalue - Expectation value
-- bit_score - Bit score of alignment
-- ko_id - KEGG Orthology (KO) identifier
-- ko_name - KO name
-- EC - Enzyme Commission (EC) assignment from KO
-- img_ko_flag - 'Yes' (assigned by IMG pipeline); 'No' - from KEGG.

<taxon_oid>.signalp.tab.txt (SignalP)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- feature_type - "cleavage"
-- start_coord - start coordinate of feature
-- end_coord - end coordinate of feature

<taxon_oid>.tmhmm.tab.txt (TMHMM)
-- gene_oid - Gene object identifier of query gene
-- gene_length - Length of protein sequence
-- feature_type - feature
-- start_coord - start coordinate of feature
-- end_coord - end coordinate of feature

<taxon_oid>.xref.tab.txt
-- gene_oid - Gene object identifier of query gene
-- db_name - External database
-- id - External ID corresponding to database

<taxon_oid>.crispr.txt (optional)
-- contig_id - Contig/Scaffold ID
-- crispr_no - CRISPR number
-- pos - Starting position of array element
-- repeat_seq - Repeat sequence
-- spacer_seq - Spacer sequence
-- tool_code - Single letter code for tool used

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license: cc-by-4.0