Package: assemblyStatistics
assemblyStatisticsA script to evaluate the assembly of a given genome.💙 If you like this project, give it a ⭐ and share it with friends!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。⚙ USAGEassemblyStatistics -f test.fasta -l 100
assemblyStatistics test.fasta⚡ Quick installpip install assemblyStatistics🔧 OptionsrunassemblyStatistics -horassemblyStatistics --helpfor optionsUsage: 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 outputDefault 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                    5JSON format output with commandassemblyStatistics -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/IssuesPlease report any issues to theissues pageor emaillinwenchao@yeah.netTodoGet statistics from a list of filesCompressed format (.gz, .bz2 or .xz) supportMultiple output format support