#spades_stats
Calculating statistics for SPAdes assemblies based on the coverage and length found in the fasta description line.
By Karin Lagesen | @karinlag
How to run
###Requirements
- Python 2.7
- Biopython
###Command line
usage: spades_stats.py [-h] [-d DIRECTORY] [-p STRING]
optional arguments:
-h, --help show this help message and exit
-d DIRECTORY, --directory DIRECTORY
Directory containing directories with scaffolds.fasta
in them
-p STRING, --prefix STRING
Prefix string for output files
###Input
The input for this code is a directory where there are spades assemblies. The code locates all files named "scaffolds.fasta" under that directory and calculates statistics for that file.
###Output
Statistics is calculated for each file, and the results are written to one output file. The output file will be prefixed with string given to option -p.
The output is output one line per scaffolds file, with the following columns (first line is header line):
| Column | Description |
|---|---|
| Scaffolds_filename | name of input file, incl relative path |
| N50 | N50 value for assembly |
| #contigs>=N50 | the fewest number of contigs whose sum makes up N50 |
| coverage_contigs | average coverage over the #contigs>=N50 |
Next comes five number statistics for length and coverage. The five stats calculated are(in order):
- min: minimum value (length or coverage)
- max: maximum value (length or coverage)
- avg: average value (length or coverage)
- median: median value (length or coverage)
- std: standard deviation (length or coverage)
##Issues
Please report problems here: https://github.com/karinlag/spades_stats/issues
##License
Please read the LICENSE included in the repository