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是一个可以从NCBI SRA, MG-RAST和iMicrobe数据库批量下载数据的工具，2020年发表在Bioinformatics 杂志，可下载sra数据并直接转换为fastq文件
其转化依赖于fasterq-dump或fastq-dump，因此安装前注意要下载sra-tools：conda install -c bioconda sra-tools
还要注意其他依赖条件有python3环境、sra-tools版本大于2.9、pigz和wget
1 下载安装
conda安装：
conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge 或者pip安装：
pip install grabseqs 2 使用
2.1 详尽参数：
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个线程，保存数据到proj/metadata.csv，下载到文件夹 proj/，下载失败重试的次数为3，从SRP#######获取所有样本
# 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********* - 如果想将参数传递给fastq -dump获取数据，可以这样做:
# 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" 其他常用命令的简单示例：
- 从单个SRA项目下载所有样本
#Download all samples from a single SRA Project: grabseqs sra SRP******** - 或者结合其他各类项目一起下载
#Or any combination of projects (S/ERP), runs (S/ERR), BioProjects (PRJNA): grabseqs sra SRR******** ERP******** PRJNA******** ERR******** - 只想获取样本编号的话使用 -l 参数
#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******** - 从 MG-RAST、iMicrobe数据库下载数据也是类似用法，(样本编号前加“s”，项目编号前加“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 
