Filtering

Filters are applied during ingestion to control which records are imported into the database. This reduces database size and processing time.

Taxonomy filters

# Human only (NCBI taxonomy ID 9606)
srake ingest --auto --taxon-ids 9606

# Multiple species
srake ingest --auto --taxon-ids 9606,10090,7955

# By organism name
srake ingest --auto --organisms "Homo sapiens"

# Exclude specific taxa
srake ingest --auto --exclude-taxon-ids 32630

Platform and library filters

# Illumina RNA-Seq
srake ingest --auto --platforms ILLUMINA --strategies RNA-Seq

# Multiple platforms
srake ingest --auto --platforms ILLUMINA,PACBIO_SMRT

# Multiple strategies
srake ingest --auto --strategies RNA-Seq,WGS,ChIP-Seq

Supported platforms: ILLUMINA, PACBIO_SMRT, OXFORD_NANOPORE, ION_TORRENT, ABI_SOLID, LS454, BGISEQ, COMPLETE_GENOMICS, HELICOS, CAPILLARY.

Date range filters

# Records from 2024 only
srake ingest --auto --date-from 2024-01-01 --date-to 2024-12-31

# Everything after a date
srake ingest --auto --date-from 2023-06-01

Sequencing metrics

# Minimum 10 million reads
srake ingest --auto --min-reads 10000000

# Read count range
srake ingest --auto --min-reads 1000000 --max-reads 100000000

# Minimum 1 billion bases
srake ingest --auto --min-bases 1000000000

Combining filters

All filters use AND logic:

srake ingest --auto \
  --taxon-ids 9606 \
  --platforms ILLUMINA \
  --strategies RNA-Seq \
  --date-from 2024-01-01 \
  --min-reads 10000000

Preview mode

Use --stats-only to see what would be imported without actually inserting data:

srake ingest --auto --taxon-ids 9606 --stats-only

Use --filter-verbose to see per-record filter decisions during ingestion.

Resume