Host depletion
Host depletion filters sequencing reads to remove (or isolate) reads that match a host genome index, retaining the reads of interest for downstream analysis. Sparrowhawk uses Deacon (preprint) for this purpose.
General considerations
- Requires uploading a pre-built Deacon index (
.dcifile) for the host genome of interest. The Deacon repository contains pre-built indexes for common hosts (human, etc.). - Accepts FASTQ reads (plain or gzipped); output is written in the same format (optionally gzip-compressed).
- The two thresholds (absolute and relative) are applied together: a read must satisfy both to be classified as host-derived.
Parameters
The values in brackets are the default ones:
- Deplete mode [enabled]: when enabled, reads matching the host index are removed from the output. When disabled, matching reads are kept instead (useful for isolating host reads).
- Absolute threshold [1]: integer 1–50; minimum number of k-mers that must match the host index for a read to be classified as host-derived.
- Relative threshold [0.05]: real 0–1; minimum proportion of a read’s k-mers that must match the host index.
Example
The following data can be used to try out host depletion:
- Human host index (pre-built, panhuman-1, k=31 w=61): panhuman-1.k31w61.idx
- Reads to deplete (as a test FASTA): Klebsiella pneumoniae assembly GCA_004138665.1