parallel-fastq-dump --sra-id SRR2244401 --threads 4 --outdir out/ --split-files --gzip --threads 4设置线程为4 实测parallel-fastq-dump是最快的。 4 10X测序使用的参数 fastq-dump --split-files fasterq-dump --split-files --include-technical parallel-fastq-dump --split-files 这个还是参考知...
② fasterq-dump + pigz 用时:11m12s(注意fasterq-dump处理10x数据的参数是--split-files --include-technical,仅加--split-files得不到三个文件 ) time ( fasterq-dump -e 12 -O ./ --split-files --include-technical SRR7722937.sra ; pigz -p 12 *fastq) ③ parallel-fastq-dump(--gzip) 用时:...
--skip-technical skip technical reads --include-technical include technical reads -P|--print-read-nr print read-numbers -M|--min-read-len filter by sequence-len --table which seq-table to use in case of pacbio --strict terminate on invalid read ...
time(fasterq-dump-e12-O./--split-files--include-technicalSRR7722937.sra;pigz-p12*fastq) ③ parallel-fastq-dump(--gzip) 用时:4m2s (处理10x数据的参数与fastq-dump一致,仅用--split-files即可) time(parallel-fastq-dump-t12-O./--split-files--gzip-sSRR7722937.sra) 通过以上测试,可以看到parallel...
For details, see FASTQ/FASTA split file. By default, the reads refer to biological reads only. However, if you set IncludeTechnical to true, then the software also includes the technical reads in the output files. Data Types: char | string...
fasterq-dump SRRXXXXXX --concatenate-reads --include-technical Here are some important differences tofastq-dump: The-Z|--stdoutoption does not work for split-3 and split-files. The tool will fall back to producing files in these cases. ...
For details, see FASTQ/FASTA split file. By default, the reads refer to biological reads only. However, if you set IncludeTechnical to true, then the software also includes the technical reads in the output files. Data Types: char | string...
fasterq-dump SRRXXXXXX --concatenate-reads --include-technical Here are some important differences tofastq-dump: The-Z|--stdoutoption does not work for split-3 and split-files. The tool will fall back to producing files in these cases. ...
fastq-dump、fasterq-dump和parallel-fastq-dump处理SRA文件的速度比较 - 知乎 注意fasterq-dump处理10x数据的参数是--split-files --include-technical,仅加--split-files得不到三个文件 fasterq-dump-e48-O./-b 200MB-c 400MB-m 4000MB--split-files--include-technicalSRR28995922.sra;pigz-p48*fastq ...
column)--skip-technical skip technical reads--include-technical explicitly include technical reads-P|--print-read-nr include read-numberindefline-M|--min-read-len<count>filterby sequence-lenght--table<name>which seq-table to useincase of pacbio--strict terminate on invalid read-B|--bases<bas...