NGS-statter 1.14.0

A collection of utilities for computing statistics on genomic sequences and alignments.

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

Commands

use 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