assemblyStatistics

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。

⚙ USAGE

assemblyStatistics -f test.fasta -l 100
assemblyStatistics test.fasta

⚡ Quick install

pip install assemblyStatistics

🔧 Options

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]

Sample output

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
    }
}

Feedback/Issues

Please report any issues to the issues page or email linwenchao@yeah.net

Todo

• Get statistics from a list of files
• Compressed format (.gz, .bz2 or .xz) support
• Multiple output format support