Synopsis
A simple program for evaluate the assembly of a give genome. Shows simple statistics about a fasta file containing many sequences. The result includes the name, N50, N90, GC Content, N rate, number of sequences etc., as well as various other information both in large scaffolds (>1000 bp) and in all sequences.
USAGE
Usage: assemblyStatics.py [options] -f INPUT.fasta
Options:
-h, --help show this help message and exit
-f FILE, --fasta=FILE
input fasta file
-L LARGE, --large=LARGE
Threshold of LARGE sequence [default = 1000]
python assemblyStatics.py -f duixia.SSPACE2.final.scaffolds_new.fasta
Sample output
All scaffold sequences summary:
-----------------------------------
Counts of scaffold sequences: 16551
Length of scaffold sequences: 1413526492
Largest scaffold name: scaffold229_size1132254|ref0002838
Largest scaffold length: 1132254
Scaffold N50: 154152
Counts of N50: 2599
Scaffold N90: 40011
Counts of N90: 9491
GC content(%): 35.88%
N content (%): 4.018%
LARGE (>1000bp) sequences summary:
-----------------------------------
Counts of LARGE sequences: 16549
Length of LARGE sequences: 1413524983
LARGE scaffold N50: 154152
Counts of LARGE N50: 2599
LARGE scaffold N90: 40011
Counts of LARGE N90: 9491
GC content(%): 35.88%
N content (%): 56805%
contigs summary:
-----------------------------------
Counts of contigs: 36707
Maximum length of contigs: 848414
contig N50: 59299
Counts of contig N50: 6486
contig N90: 16287
Counts of contig N90: 23604