A script to evaluate the assembly of a given genome.
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It provides various statistics regarding a Fasta file containing multiple sequences, such as sequence name, N50, N90, GC Content, N rate, etc., both large scaffolds (>1000 bp) and contigs across all sequences.
一个用于评估给定基因组的拼接结果的脚本，用于查看拼接结果的Scaffold， Contig统计信息。它提供了有关包含多个序列的Fasta文件的各种统计信息，如序列名称、N50、N90、GC含量、N比率、序列数量等。
assemblyStatistics -f test.fasta -l 100
assemblyStatistics test.fasta
pip install assemblyStatistics
run assemblyStatistics -h or assemblyStatistics --help for options
Usage: assemblyStatistics [options] -f INPUT.fasta
A script to evaluate the assembly of a given fasta.
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-f FILE, --fasta=FILE
input fasta file
-t FORMAT, --outfmt=FORMAT
format of the output, choices = [txt, json]
-l LENGTH, -L LENGTH, --length=LENGTH
Threshold of length defined a sequence as Large
[default = 1000]
Default txt output(human readable text format)
All scaffold sequences summary:
--------------------------------------------------
Counts of scaffold sequences 3
Length of scaffold sequences 490
Largest scaffold name seq1
Largest scaffold length 210
Scaffold N50 210
Counts of N50 2
Scaffold N90 70
Counts of N90 3
GC content(%) 42.86
N Length 141
N content (%) 28.78
LARGE (> 100 bp) sequences summary:
--------------------------------------------------
Counts of LARGE sequences 2
Length of LARGE sequences 420
LARGE scaffold N50 210
Counts of LARGE N50 1
LARGE scaffold N90 210
Counts of LARGE N90 2
GC content(%) 33.33
N Length 141
N content (%) 33.57
contigs summary:
--------------------------------------------------
Counts of contigs 7
Maximum length of contigs 70
contig N50 70
Counts of contig N50 3
contig N90 36
Counts of contig N90 5 JSON format output with command assemblyStatistics -f sample.fasta -t json
{
"All scaffolds": {
"Counts of scaffold sequences": 4,
"Length of scaffold sequences": 605,
"Largest scaffold name": "seq2",
"Largest scaffold length": 271,
"Scaffold N50": 269,
"Counts of N50": 2,
"Scaffold N90": 45,
"Counts of N90": 3,
"GC content(%)": 49.09090909090909,
"N Length": 59,
"N content (%)": 9.75206611570248
},
"LARGE sequences": {
"threshold": 1000,
"Counts of LARGE sequences": 0,
"Length of LARGE sequences": 0
},
"Contigs": {
"Counts of contigs": 8,
"Maximum length": 225,
"contig N50": 121,
"Counts of contig N50": 2,
"contig N90": 21,
"Counts of contig N90": 6
}
}Please report any issues to the issues page or email [email protected]
- Get statistics from a list of files
- Compressed format (.gz, .bz2 or .xz) support
- Multiple output format support