sample
Commands under this group are meant to be used as a part of an NGS data processing pipeline, to generate read statistics at different stages (trimming, pre-processing, alignment etc) of the pipeline, and finally combine them into a single tsv file for all the samples in the pipeline, for the final report.
sample-stats
Aggregate read statistics from various steps in the workflow for a single sample into a json file.
Options
option |
description |
required |
default value |
|---|---|---|---|
–sample-name |
Sample name |
✓ |
|
–raw-reads |
Path to seqkit stats output for raw reads |
✓ |
|
–first-trim |
Path to seqkit stats output for reads after first trimming step |
✓ |
|
–second-trim |
Path to seqkit stats output for reads after second trimming step |
✗ |
|
–rRNA-mapped |
Path to seqkit stats output for reads mapped to rRNA reference |
✗ |
|
–rRNA-free |
Path to seqkit stats output for reads not mapped to rRNA reference |
✗ |
|
–align-stats |
Path to bam statistics json file generated using STAR command |
✓ |
|
–dedup-stats |
Path to bam statistics json file after UMI deduplication generated using STAR command |
✗ |
|
–kraken2-report |
Path to kraken2 report file |
✗ |
|
–out-json |
Output json file for collected statistics |
✓ |
Usage
ngs-statter sample-stats --sample-name SAMPLE_NAME --raw-reads path/to/raw_reads_stats.txt --first-trim path/to/first_trim_stats.txt --align-stats path/to/align_stats.json --out-json path/to/sample_stats.json
compile-stats
Aggregate read statistics for multiple samples (generated using sample-stats command) into a single tsv file for the final report.
Options
option |
description |
required |
default value |
|---|---|---|---|
–output |
Output file name for all sample statistics |
✓ |
Usage
ngs-statter compile-stats --output path/to/compiled_stats.tsv path/to/sample1_stats.json path/to/sample2_stats.json