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LinkStats collects, compiles and processes QC statistics on algined barcoded genomic reads. It produces CSV reports and graphical plots.

Overview

LinkStats consists of a three-stage pipeline:

1. Read any input SAM/BAM/CRAM data sources and compile linked-read data.
   • Optionally output summary and/or molecule and/or coverage data as CSV files.
2. Process data into histograms.
   • Optionally read in additional molecule and/or coverage data from CSV files.
   • Optionally ouput histogram data as CSV files.
3. Create plots from histogram data.
   • Optionally input additional histogram data from CSV files.

Usage Example

> LinkStats sam-data sample_reads.cram save-csvs results/csvs/sample save-plots results/plots/sample

This reads alignment data from the file sample_reads.cram, saves summary data to the directory results/csvs with the prefix sample_ and saves histogram plots to the directory results/plots with the prefix sample_. See manual for detailed usage instructions.

Alignment Data Requirments

Alignment data must be coordinate-sorted SAM data with barcodes as BX:Z: tags. Optional, additional barcode grouping can be made by MI:i tags. Sample names are taken from SM:Z: (preferably) or RG:Z: tags if present, or can be set with a command-line option.

Example Output

Summary Statistics

Sample Name	Genome Length	Total Alignments	Duplicates	QCFail	Unmapped	Mapped	No BX	No MI	Zero MapQ	N50 Reads Per Molecule	N90 Reads Per Molecule	auN Reads Per Molecule	No. Molecules (No. Reads >= 1)	Mean Read MapQ Per Molecule (No. Reads >= 1)	Mean Molecule Length (No. Reads >= 1)	N50 Molecule Length (No. Reads >= 1)	N90 Molecule Length (No. Reads >= 1)	auN Molecule Length (No. Reads >= 1)	No. Molecules (No. Reads >= 3)	Mean Read MapQ Per Molecule (No. Reads >= 3)	Mean Molecule Length (No. Reads >= 3)	N50 Molecule Length (No. Reads >= 3)	N90 Molecule Length (No. Reads >= 3)	auN Molecule Length (No. Reads >= 3)	No. Molecules (No. Reads >= 5)	Mean Read MapQ Per Molecule (No. Reads >= 5)	Mean Molecule Length (No. Reads >= 5)	N50 Molecule Length (No. Reads >= 5)	N90 Molecule Length (No. Reads >= 5)	auN Molecule Length (No. Reads >= 5)	No. Molecules (No. Reads >= 10)	Mean Read MapQ Per Molecule (No. Reads >= 10)	Mean Molecule Length (No. Reads >= 10)	N50 Molecule Length (No. Reads >= 10)	N90 Molecule Length (No. Reads >= 10)	auN Molecule Length (No. Reads >= 10)	Median Insert Size	Mean Short Read Depth	Mean Short Read Depth Per Molecule (No. Reads >= 1)	Molecule Read Depth (No. Reads >= 1)	Mean Short Read Depth Per Molecule (No. Reads >= 3)	Molecule Read Depth (No. Reads >= 3)	Mean Short Read Depth Per Molecule (No. Reads >= 5)	Molecule Read Depth (No. Reads >= 5)	Mean Short Read Depth Per Molecule (No. Reads >= 10)	Molecule Read Depth (No. Reads >= 10)
sample_1	475288177	76630734	0.31437793614243603	0.0	0.020081903430547852	0.9799180965694522	0.02013981753065291	0.02013981753065291	0.18363639841946444	2	2	4.508073122000967	14206313	35.64287354551842	3552.3337376840846	28158	5566	31222.761770932833	3026475	42.63248095789803	15475.771771780703	29732	8844	33071.83794352541	1290033	45.54367534814054	23451.85308205294	34597	12794	38466.78045604522	312474	47.91390010477723	36652.9717896529	45269	21138	49249.24314427641	207	23.94266163073524	1.0525249483701045	106.1788771530919	0.27878003867807977	98.54450129315967	0.12086867821999131	63.65330730076208	0.07543374059593067	24.097171487183868
sample_2	2782012602	589796532	0.7195109838319632	0.0	0.015188315824142554	0.9848116841758574	0.01340242027737118	0.01340242027737118	0.034898881026312986	8	2	14.249821430536441	29550007	45.66036275340808	6104.185723543145	37299	9131	42537.54489314595	9470847	47.529572485517356	18313.300594867596	38452	11597	43997.00931155544	5978121	49.441155002674705	25248.238797943366	41386	14216	47093.63476301429	3164327	50.59626523246061	35413.34951065424	47624	19803	53344.70567932435	271	31.482526333286536	0.9676011811817129	64.83749596616673	0.5293547845761889	62.344242392831546	0.33715994721512627	54.254616410612506	0.19225956277851122	40.27998217421447

Molecule Data

Sample Name	Molecule Length	No. Reads	MI	BX	Reference	Mean Read Depth	Mean MapQ	No. Gaps	Mean Gap Size	Max Gap Size
sample_1	151	1	42.0	AAACTTATAAACAAAT-1	SUPER_2	0.9933774834437086	39.0	0	0.0	0
sample_1	693	2	62.0	AAACTTATAAACAAAT-1	SUPER_2	0.42857142857142855	60.0	1	396.0	396
sample_1	147	2	0.0	AAACTTATAAACAACA-1	SUPER_2	2.020408163265306	52.0	0	0.0	0

Coverage Gap Data

Sample Name	Reference	Gap Length
sample_1	SUPER_2	492
sample_1	SUPER_2	503
sample_1	SUPER_2	85

Molecule Length Histogram Data

PDF	CDF	Molecule Length	Sample Name	Min No. Reads
9.367449744132983e-06	1.3014845860860104e-05	96.0	sample_1	1
0.0012569059966509256	0.0017593212851612847	109.5	sample_1	1
0.0010904307120362616	0.0032743320967205856	110.5	sample_1	1

Coverage Gap Histogram Data

PDF	CDF	Coverage Gap Length	Sample Name
0.014091511936339523	0.01579554609844439	1.5	sample_1
0.011836098945160693	0.029062940495769775	2.5	sample_1
0.011832243538338165	0.04232601326625564	3.5	sample_1

Molecule Length PDFs

Molecule Length CDFs

Coverage Gap PDFs

Coverage Gap CDFs