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
