NGS statter
A package to compute read/alignment statistics per fastq/bam files. This package is used as a part of an NGS analysis pipeline to generate intermediate QC results and final alignment statistics for all samples.
Parsers
- Fastq parser
- GFF parser
- BAM parser
- kraken2 report aggregator
- fastp fastp trimming stats aggregator
- STAR aligner alignment stats to json
- parser fix UMI position in flexbar fastqs
Plotting functions
- Fastq read length distribution plot
- Overall aligned read length distribution plot
- Gene type specific read length distribution plot
- Alignment statistics
Installation
This package can be installed using pip:
$ pip install ngs-statter
Documentation
A detailed documentation is available at this read the docs page. A brief description of various commands available in this package is given below
Commands
use ngs-statter -h for a list of available helper commands.
Commands are grouped based on the input as follows:
alignment
Parse alignment (.bam) files and generate base statistics
| command | description | usage |
|---|---|---|
| bam | Compute basic alignment statistics for a generic BAM file | ngs-statter bam -h |
| STAR | Compute alignment statistics for a STAR aligned BAM file and output as JSON | ngs-statter STAR -h |
crosslink
Parse output crosslink (.bed) files from Shoji or htseq-clip
| command | description | usage |
|---|---|---|
| csv-meta-example | Print example CSV metadata file for crosslink plotting to console | ngs-statter csv-meta-example -h |
| count-crosslinks | Count crosslinking sites over secondary structure/primary motif regions | ngs-statter count-crosslinks -h |
| crosslink-line-plot | Plot crosslinking sites over secondary structure/primary motif regions as line plots | ngs-statter crosslink-line-plot -h |
| crosslink-heatmap | Plot crosslinking sites over secondary structure/primary motif regions as heatmaps | ngs-statter crosslink-heatmap -h |
fastq
Parse fastq files to compute and plot read-length distributions
| command | description | usage |
|---|---|---|
| parse-read-length | Compute fastq read length distribution | ngs-statter parse-read-length -h |
| plot-read-length | Read in json formatted output files (from parse-read-length) and output html plot |
ngs-statter plot-read-length -h |
flexbar
Fix the position of UMIs in flexbar output fastq files
| command | description | usage |
|---|---|---|
| fix-header | Fix flexbar UMI headers | ngs-statter fix-header -h |
genetype
Given a gff3 formatted gene annotation file and an alignment (.bam) file, compute and plot read-length distribution of reads aligning to gene types (protein coding, lncRNA,...).
| command | description | usage |
|---|---|---|
| parse-gene-type-read-length | Compute gene type read length distributions | ngs-statter parse-gene-type-read-length -h |
| plot-gene-type-read-length | Plot gene type read length distributions using outputs from parse-gene-type-read-length |
ngs-statter plot-gene-type-read-length -h |
kraken
Given NCBI taxonomy files and a set of Kraken2 species classification reports, merge the reports into one single output.
| command | description | usage |
|---|---|---|
| collect-reports | Collect kraken2 reports into a single file | ngs-statter collect-reports -h |
sample
| command | description | usage |
|---|---|---|
| sample-stats | Collect statistics from various steps in a workflow (trimming, alignment,...) and compile into a single json file | ngs-statter sample-stats -h |
| compile-stats | Collect stats from multiple samples (output from sample-stats) into a single tsv file |
ngs-statter compile-stats -h |
Hentze Group, EMBL Heidelberg
1 maintainer
Metadata
1 maintainer
Release files for NGS-statter 1.20.3
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| File | Interpreter | ABI | Platform | Reset |
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| ngs_statter-1.20.3-cp312-cp312-manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.28+ x86-64 | Details |
Release files / ngs_statter-1.20.3-cp312-cp312-manylinux_2_28_x86_64.whl
| Download URL | ngs_statter-1.20.3-cp312-cp312-manylinux_2_28_x86_64.whl |
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| Size | 3.7 MB |
| Tags | CPython 3.12 Linux glibc 2.28+ x86-64 |
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