下载和安装
https://sourceforge.net/projects/soapdenovo2/files/GapCloser/

使用

GapCloser -a scaffolds.fasta -b input_library.txt -o gapcloser_scaffolds.fasta -l 149 -t 4

需要编辑input文件

#maximal read length
max_rd_len=149
[LIB]
#average insert size
avg_ins=408
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=4
#use only first 100 bps of each read
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/mnt/e/linux/experiment/data/fastp/corrected_cutf_uni_10m_1.fastq
q2=/mnt/e/linux/experiment/data/fastp/corrected_cutf_uni_10m_2.fastq