How to calculate A-statistic in an assembly?

hicham

Member

Join Date: Feb 2010

Posts: 14
- Share
- Tweet
#1

How to calculate A-statistic in an assembly?

02-09-2010, 01:56 PM

Hi,

I have a problem and I can't find a solution to it anywhere.

In hawkeye (assembly visualisation sofware of Amos), we can see a graphic of "coverage stat" that correspond to the A-statistic parameter. I want to calculate this statistic in all points of the contig like in this softwtare.

I finded a PDF in internet that explaine how to calculate it:

A-statistic : Model the "arrival" of reads along the length of a unitig as a Poisson process:
G: length of genome
N: total number of reads
k: number of reads in the unitig
D : the distance between the start of the first read to the start of the
kth read

A-statistic = DN/G log (e) - k log (2)

Anyway, I can't applicate it in differents points of contig so that I can create a graphic.

Somebody can give me some explination or example to calculate it?

Thank you very much
Tags: None

Previous template Next

Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
- Channel: Articles
Today, 11:43 AM
Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM
From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data

by SEQadmin2

Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...
- Channel: Articles
06-02-2026, 10:05 AM

Topics	Statistics	Last Post
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2 Started by SEQadmin2, Yesterday, 05:37 AM	0 responses 7 views 0 reactions	Last Post by SEQadmin2 Yesterday, 05:37 AM
Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2 Started by SEQadmin2, 06-26-2026, 11:10 AM	0 responses 17 views 0 reactions	Last Post by SEQadmin2 06-26-2026, 11:10 AM
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, 06-17-2026, 06:09 AM	0 responses 52 views 0 reactions	Last Post by SEQadmin2 06-17-2026, 06:09 AM
Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2 Started by SEQadmin2, 06-09-2026, 11:58 AM	0 responses 110 views 0 reactions	Last Post by SEQadmin2 06-09-2026, 11:58 AM

Unconfigured Ad

How to calculate A-statistic in an assembly?

Latest Articles

ad_right_rmr

News