https://bitbucket.org/rirgabiss/mhinngs/src/master/
MHinNGS is a tool for analysis of microhaplotypes (MHs) in singleend sequencing data obtained through a massive parallel sequencing plattform (MPS). The tool identifies the reads with the MHs and calls the genotypes of the MHs according to the criteria and positions specified in the configuration file. It also searches for additional variants in the region defined by the start and the stop positions specified in the configuration file.
这个软件的输入是参考序列和原始单端测序的fastq 包括了比对过程 依赖的第三方软件包括
python 3.6 including pip
samtools version 1.9
hisat2 version 2.1.0
stringtie version 2.0.3
agrep T.R.E. version 0.8.0
不支持双端序列