grabseqs——批量下载sra数据并直接转换为fastq文件的工具 - 简书 (jianshu.com)

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)

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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

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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

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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