版本：0.20.1
fastp之前的版本不支持拼接，

-m, --merge          for paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.
    --merged_out         in the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output (string [=])
    --include_unmerged   in the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default.
-c, --correction                     enable base correction in overlapped regions (only for PE data), default is disabled
    --overlap_len_require            the minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default. (int [=30])
    --overlap_diff_limit             the maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default. (int [=5])
   --overlap_diff_percent_limit     the maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%. (int [=20])

本次测试的数据为PE250，共85,109对reads。

mkdir -p fastp
mkdir -p SE
ls *1.fastq.gz|while read id;
do
fastp -m -c --overlap_len_require 10 \
--overlap_diff_percent_limit 25 \
-i ${id%_*}_R1.fastq.gz -I ${id%_*}_R2.fastq.gz \
--merged_out ./SE/${id%_*}.clean.fq.gz \
--out1 ./SE/${id%_*}.unmerge1.fq.gz --out2 ./SE/${id%_*}.unmerge2.fq.gz \
-j ./fastp/${id%_*}.json -h ./fastp/${id%_*}.html;
done

主要参数说明：

-m开启merge模式；
-c 校准重叠区域内的碱基；
--overlap_len_require 设置重叠区最小长度；
--overlap_diff_limit 设置重叠区域的最大不匹配碱基数
--overlap_diff_percent_limit 设置重叠区域最大不匹配碱基数百分比

fastp拼接得到62,925条tag，未拼接成功21,543对reads。

mkdir -p flash
ls *1.fastq.gz |while read id;
do
flash ${id%_*}_R1.fastq.gz -O ${id%_*}_R2.fastq.gz \
-m 10 -M 100 -x 0.25 -z -o ${id%_*} -d ./flash
done

主要参数说明：

-m 拼接时overlap区的最小长度阈值，默认10bp；
-M 拼接时overlap区的最大长度阈值，默认65bp；
-x 拼接时overlap区允许的最大碱基错配比率（最大碱基错配数目/overlap区长度），默认为0.25；
-z 压缩输出文件；
-d 输出文件存放目录，默认当前工作目录

flash拼接得到78,054条tag，未拼接成功7,055对reads。

挑选一条tag比对拼接质量

image.png

fastp和flash拼接都得到一条445 bp的tag，唯一不同的是，在tag的257位，二者拼接的碱基不一样，查看原始序列
R1

R1.png

R2

R2.png