- spades安装
(base) 202031107010173@xiaoming-HP:~$ tar zvxf /disk1/shares/SPAdes-3.12.0-Linux.tar.gz -C ~/Biosofts/
(base) 202031107010173@xiaoming-HP:~$ cd Biosofts
(base) 202031107010173@xiaoming-HP:~/Biosofts$ cd SPAdes-3.12.0-Linux/
(base) 202031107010173@xiaoming-HP:~/Biosofts/SPAdes-3.12.0-Linux$ cd bin
(base) 202031107010173@xiaoming-HP:~/Biosofts/SPAdes-3.12.0-Linux/bin$ ./spades.py -h
(base) 202031107010173@xiaoming-HP:~/Biosofts/SPAdes-3.12.0-Linux/bin$ pwd
/disk1/202031107010173/Biosofts/SPAdes-3.12.0-Linux/bin
(base) 202031107010173@xiaoming-HP:~/Biosofts/SPAdes-3.12.0-Linux/bin$ echo 'export PATH=~/Biosofts/SPAdes-3.12.0-Linux/bin:$PATH' >> ~/.bashrc
(base) 202031107010173@xiaoming-HP:~/Biosofts/SPAdes-3.12.0-Linux/bin$ source ~/.bashrc
(base) 202031107010173@xiaoming-HP:~$ spades.py -h
spades.py -h命令后的显示结果
Usage: /disk1/202031107010173/Biosofts/SPAdes-3.12.0-Linux/bin/spades.py [options] -o <output_dir>
Basic options:
-o <output_dir> directory to store all the resulting files (required)
--sc this flag is required for MDA (single-cell) data
--meta this flag is required for metagenomic sample data
--rna this flag is required for RNA-Seq data
--plasmid runs plasmidSPAdes pipeline for plasmid detection
--iontorrent this flag is required for IonTorrent data
--test runs SPAdes on toy dataset
-h/--help prints this usage message
-v/--version prints version
Input data:
--12 <filename> file with interlaced forward and reverse paired-end reads
-1 <filename> file with forward paired-end reads
-2 <filename> file with reverse paired-end reads
-s <filename> file with unpaired reads
--merged <filename> file with merged forward and reverse paired-end reads
--pe<#>-12 <filename> file with interlaced reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-1 <filename> file with forward reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-2 <filename> file with reverse reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-s <filename> file with unpaired reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-m <filename> file with merged reads for paired-end library number <#> (<#> = 1,2,...,9)
--pe<#>-<or> orientation of reads for paired-end library number <#> (<#> = 1,2,...,9; <or> = fr, rf, ff)
--s<#> <filename> file with unpaired reads for single reads library number <#> (<#> = 1,2,...,9)
--mp<#>-12 <filename> file with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-1 <filename> file with forward reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-2 <filename> file with reverse reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-s <filename> file with unpaired reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-<or> orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--hqmp<#>-12 <filename> file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-1 <filename> file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-2 <filename> file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-s <filename> file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-<or> orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--nxmate<#>-1 <filename> file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--nxmate<#>-2 <filename> file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--sanger <filename> file with Sanger reads
--pacbio <filename> file with PacBio reads
--nanopore <filename> file with Nanopore reads
--tslr <filename> file with TSLR-contigs
--trusted-contigs <filename> file with trusted contigs
--untrusted-contigs <filename> file with untrusted contigs
Pipeline options:
--only-error-correction runs only read error correction (without assembling)
--only-assembler runs only assembling (without read error correction)
--careful tries to reduce number of mismatches and short indels
--continue continue run from the last available check-point
--restart-from <cp> restart run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc', 'last')
--disable-gzip-output forces error correction not to compress the corrected reads
--disable-rr disables repeat resolution stage of assembling
Advanced options:
--dataset <filename> file with dataset description in YAML format
-t/--threads <int> number of threads
[default: 16]
-m/--memory <int> RAM limit for SPAdes in Gb (terminates if exceeded)
[default: 250]
--tmp-dir <dirname> directory for temporary files
[default: <output_dir>/tmp]
-k <int,int,...> comma-separated list of k-mer sizes (must be odd and
less than 128) [default: 'auto']
--cov-cutoff <float> coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
--phred-offset <33 or 64> PHRED quality offset in the input reads (33 or 64)
[default: auto-detect]
- spades 组装基因组
(base) 202031107010173@xiaoming-HP:~$ spades.py --careful --pe1-1 /disk1/shares/Seqs/test_7942raw_1.fq.gz --pe1-2 /disk1/shares/Seqs/test_7942raw_2.fq.gz -o ./SPAdesout
Command line: /disk1/202031107010173/Biosofts/SPAdes-3.12.0-Linux/bin/spades.py --careful --pe1-1 /disk1/shares/Seqs/test_7942raw_1.fq.gz --pe1-2 /disk1/shares/Seqs/test_7942raw_2.fq.gz -o /disk1/202031107010173/SPAdesout
（中间省略加载过程保留最后部分）
===== Mismatch correction finished.
* Corrected reads are in /disk1/202031107010173/SPAdesout/corrected/
* Assembled contigs are in /disk1/202031107010173/SPAdesout/contigs.fasta
* Assembled scaffolds are in /disk1/202031107010173/SPAdesout/scaffolds.fasta
* Assembly graph is in /disk1/202031107010173/SPAdesout/assembly_graph.fastg
* Assembly graph in GFA format is in /disk1/202031107010173/SPAdesout/assembly_graph_with_scaffolds.gfa
* Paths in the assembly graph corresponding to the contigs are in /disk1/202031107010173/SPAdesout/contigs.paths
* Paths in the assembly graph corresponding to the scaffolds are in /disk1/202031107010173/SPAdesout/scaffolds.paths
======= SPAdes pipeline finished.
SPAdes log can be found here: /disk1/202031107010173/SPAdesout/spades.log
