Filtering is performed using BBTools rqcfilter.sh script.

## Fastq Files

| Number of Reads | File Size | File Location
--- | --- | --- | ---
Input FASTQ | [_RAW-READ-CNT_] | [_RAW-FILE-SIZE_] MB | [_RAW-FILE-LOCATION_]
Filtered FASTQ | [_FILTERED-READ-CNT_] | [_FILTERED-FILE-SIZE_] MB | [_FILTERED-FILE-LOCATION_]
Filtered % | [_REMOVED-READ-PCT_]% | - | -

The file size for the filtered fastq is significantly smaller than the input fastq because the reads were re-ordered to optimize gzip file compression.

## Filtering Metrics

Metric | Read Count | Base Count
--- | --- | ---
Input | [_RAW-READ-CNT_] | [_RAW-BASE-CNT_]
Remaining | [_FILTERED-READ-CNT_] | [_FILTERED-BASE-CNT_]
Percentage Removed | [_REMOVED-READ-PCT_]% | [_REMOVED-BASE-PCT_]%

Metric | Percent | Read Count
--- | --- | ---
Low Quality Removed | [_LOW-QUAL-REMOVED-PCT_] | [_LOW-QUAL-REMOVED-READ-CNT_]
Artifact Removed | [_ARTI-REMOVED-PCT_] | [_ARTI-REMOVED-READ-CNT_]
Ribosomal RNA Removed | [_RRNA-REMOVED-READ-PCT_] | [_RRNA-REMOVED-READ-CNT_]
Microbial Removed | [_MICROBE-REMOVED-READ-PCT_] | [_MICROBE-REMOVED-READ-CNT_]
Human Filtered | [_HUMAN-REMOVED-READ-PCT_] | [_HUMAN-REMOVED-READ-CNT_]
Dog Filtered | [_DOG-REMOVED-READ-PCT_] | [_DOG-REMOVED-READ-CNT_]
Cat Filtered | [_CAT-REMOVED-READ-PCT_] | [_CAT-REMOVED-READ-CNT_]
Mouse Filtered | [_MOUSE-REMOVED-READ-PCT_] | [_MOUSE-REMOVED-READ-CNT_]

[_FILTERED-READ-QC_]