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Welcome to the spore-to-VO wiki page. Here, you will find code snippets used for characterizing 14 novel species isolated from the NASA cleanroom Spacecraft Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL), California, during the Mars 2020 mission spacecraft assembly.

1. Genome Assembly

2. Overall Genome Related Indices (OGRI) Calculation

We retrieved all validly published representative genomes of the identified genera from NCBI using the command-line tool BIT (https://github.com/AstrobioMike/bit) along with NCBI Entrez-Direct.

installation

conda install -c bioconda entrez-direct conda install -c conda-forge -c bioconda -c defaults -c astrobiomike bit

esearch to get the list of representative species accession IDs

esearch -query '[ORGN] AND "representative genome"[filter] AND all[filter] NOT anomalous[filter]' -db assembly | esummary | xtract -pattern DocumentSummary -def "NA" -element AssemblyAccession > _repr.txt

bit to fetch the genomes

bit-dl-ncbi-assemblies -w _repr.txt -f fasta -j 100

unzipping

gunzip *.gz