文章：grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories | Bioinformatics | Oxford Academic (oup.com)
GitHub：louiejtaylor/grabseqs: A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA (github.com)

grabseqs是一個可以從NCBI SRA, MG-RAST和iMicrobe數據庫批量下載數據的工具，2020年發表在Bioinformatics 雜志，可下載sra數據并直接轉換為fastq文件
其轉化依賴于fasterq-dump或fastq-dump，因此安裝前注意要下載sra-tools：conda install -c bioconda sra-tools
還要注意其他依賴條件有python3環境、sra-tools版本大于2.9、pigz和wget

1 下載安裝

conda安裝：

conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge

或者pip安裝：

pip install grabseqs

2 使用

2.1 詳盡參數：

grabseqs sra [-h] [-m METADATA] [-o OUTDIR] [-r RETRIES] [-t THREADS]
             [-f] [-l] [--no_parsing] [--parse_run_ids]
             [--use_fastq_dump]
             id [id ...]

positional arguments:
  id                One or more BioProject, ERR/SRR or ERP/SRP number(s)

optional arguments:
  -h, --help        show this help message and exit
  -m METADATA       filename in which to save SRA metadata (.csv format,
                    relative to OUTDIR)
  -o OUTDIR         directory in which to save output. created if it doesn't
                    exist
  -r RETRIES        number of times to retry download
  -t THREADS        threads to use (for fasterq-dump/pigz)
  -f                force re-download of files
  -l                list (but do not download) samples to be grabbed
  --parse_run_ids   parse SRR/ERR identifers (do not pass straight to fasterq-
                    dump)
  --custom_fqdump_args CUSTOM_FQD_ARGS
                    "string" containing args to pass to fastq-dump
  --use_fastq_dump  use legacy fastq-dump instead of fasterq-dump (no
                    multithreaded downloading)

2.2 示例如下：

• 使用10個線程，保存數據到proj/metadata.csv，下載到文件夾 proj/，下載失敗重試的次數為3，從SRP#######獲取所有樣本

# use 10 threads, save metadata to proj/metadata.csv, download to the dir proj/, retry failed downloads 3x, get all samples from SRP#######)
grabseqs sra -t 10 -m metadata.csv -o proj/ -r 3 SRP*********

• 如果想將參數傳遞給fastq -dump獲取數據，可以這樣做:

# If you'd like to pass your own arguments to fasterq-dump to get data in a slightly different format, you can do so like this
grabseqs sra SRP*******  -r 0 --custom_fqdump_args="--split-spot --progress"

其他常用命令的簡單示例：

• 從單個SRA項目下載所有樣本

#Download all samples from a single SRA Project:
grabseqs sra SRP********

• 或者結合其他各類項目一起下載

#Or any combination of projects (S/ERP), runs (S/ERR), BioProjects (PRJNA):
grabseqs sra SRR******** ERP******** PRJNA******** ERR********

• 只想獲取樣本編號的話使用 -l 參數

#If you'd like to do a dry run and just get a list of samples that will be downloaded, pass -l:
grabseqs sra -l SRP********

• 從 MG-RAST、iMicrobe數據庫下載數據也是類似用法，(樣本編號前加“s”，項目編號前加“p”)

#Similar syntax works for MG-RAST:
grabseqs mgrast mgp****** mgm*******

#And iMicrobe (prefixing the sample numbers with "s" and project numbers with "p"):
grabseqs imicrobe p4 s3