[TOC]

安装环境

Ubuntu18.10
FLASH v2.2.00

安装

github上有安装介绍
https://github.com/dstreett/FLASH2

git clone https://github.com/dstreett/FLASH2.git
cd FLASH2 & make

然后可直接运行FLASH2文件夹里的flash2就可以运行。

flash2 -h

运行示例：

flash2 sim_1.fastq sim_2.fq
[FLASH] Starting FLASH v2.2.00
[FLASH] Fast Length Adjustment of SHort reads
[FLASH]  
[FLASH] Input files:
[FLASH]     sim_1.fastq
[FLASH]     sim_2.fq
[FLASH]  
[FLASH] Output files:
[FLASH]     ./out.extendedFrags.fastq
[FLASH]     ./out.notCombined_1.fastq
[FLASH]     ./out.notCombined_2.fastq
[FLASH]     ./out.hist
[FLASH]     ./out.histogram
[FLASH]  
[FLASH] Parameters:
[FLASH]     Min overlap:           10
[FLASH]     Min overlap outie:     35
[FLASH]     Max overlap:           65
[FLASH]     Max mismatch density:  0.250000
[FLASH]     Allow "outie" pairs:   true
[FLASH]     Cap mismatch quals:    false
[FLASH]     Combiner threads:      4
[FLASH]     Input format:          FASTQ, phred_offset=33
[FLASH]     Output format:         FASTQ, phred_offset=33
[FLASH]  
[FLASH] Starting reader and writer threads
[FLASH] Starting 4 combiner threads
[FLASH] Processed 25000 read pairs
[FLASH] Processed 50000 read pairs
[FLASH] Processed 75000 read pairs
[FLASH] Processed 100000 read pairs
[FLASH] Processed 125000 read pairs
[FLASH] Processed 150000 read pairs
[FLASH] Processed 175000 read pairs
[FLASH] Processed 200000 read pairs
[FLASH] Processed 225000 read pairs
[FLASH] Processed 250000 read pairs
[FLASH] Processed 275000 read pairs
[FLASH] Processed 300000 read pairs
[FLASH] Processed 325000 read pairs
[FLASH] Processed 350000 read pairs
[FLASH] Processed 375000 read pairs
[FLASH] Processed 400000 read pairs
[FLASH] Processed 425000 read pairs
[FLASH] Processed 450000 read pairs
[FLASH] Processed 475000 read pairs
[FLASH] Processed 500000 read pairs
[FLASH] Processed 525000 read pairs
[FLASH] Processed 550000 read pairs
[FLASH] Processed 575000 read pairs
[FLASH] Processed 600000 read pairs
[FLASH] Processed 625000 read pairs
[FLASH] Processed 650000 read pairs
[FLASH] Processed 675000 read pairs
[FLASH] Processed 700000 read pairs
[FLASH] Processed 725000 read pairs
[FLASH] Processed 750000 read pairs
[FLASH] Processed 775000 read pairs
[FLASH] Processed 800000 read pairs
[FLASH] Processed 825000 read pairs
[FLASH] Processed 850000 read pairs
[FLASH] Processed 875000 read pairs
[FLASH] Processed 900000 read pairs
[FLASH] Processed 925000 read pairs
[FLASH] Processed 950000 read pairs
[FLASH] Processed 975000 read pairs
[FLASH] Processed 985820 read pairs
[FLASH]  
[FLASH] Read combination statistics:
[FLASH]     Total pairs:       985820
[FLASH]     Discarded pairs:   0
[FLASH]     Percent Discarded: 0.00%
[FLASH]     Combined pairs:    183907
[FLASH]         Innie pairs:   183503 (99.78% of combined)
[FLASH]         Outie pairs:   404 (0.22% of combined)
[FLASH]     Uncombined pairs:  801913
[FLASH]     Percent combined:  18.66%
[FLASH]  
[FLASH] Writing histogram files.
[FLASH]  
[FLASH] FLASH v2.2.00 complete!
[FLASH] 8.374 seconds elapsed