source ~/miniconda3/bin/activate
conda search spades
conda install spades
Retrieving notices: ...working... done
Channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /work/home/acwnw4bl7y/miniconda3
added / updated specs:
- spades
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2026.7.16 | h06a4308_0 106 KB
certifi-2025.10.5 | py39h06a4308_0 157 KB
conda-24.11.3 | py39h06a4308_0 921 KB
openssl-3.0.17 | h5eee18b_0 5.2 MB
spades-3.13.1 | 0 13.7 MB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
------------------------------------------------------------
Total: 20.0 MB
The following NEW packages will be INSTALLED:
spades anaconda/cloud/bioconda/linux-64::spades-3.13.1-0
The following packages will be UPDATED:
ca-certificates 2024.9.24-h06a4308_0 --> 2026.7.16-h06a4308_0
certifi 2024.8.30-py39h06a4308_0 --> 2025.10.5-py39h06a4308_0
conda 24.9.1-py39h06a4308_0 --> 24.11.3-py39h06a4308_0
openssl 3.0.15-h5eee18b_0 --> 3.0.17-h5eee18b_0
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Channel "defaults" has the following notices:
[info] -- Tue Jun 9 00:00:00 2026
PyTorch 2.12 with CUDA support is now available to install with your current channel (Anaconda Main). Learn more: https://anaconda.org/main/pytorch?utm_source=channel_notices
spades.py
SPAdes genome assembler v3.13.1
Usage: /work/home/acwnw4bl7y/miniconda3/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]
