The orginial Xenome source code is available from Gossamer bioinformatics suite https://github.com/data61/gossamer

Detailed usage of Xenome is avaliable at The https://github.com/data61/gossamer/blob/master/docs/xenome.md

xenome index -T 8 -P <index_prefix> -H <mouse_mm10.fa> -G <human_hg38.fa>

xenome classify -T 8 -P <index_prefix> --pairs --host-name mouse --graft-name human -i <in_1.fastq> -i <in_2.fastq>

The reads classified into human (graft) are mapped to human genome (hg38) using HISAT2. The reads classified into mouse (host) are mapped to mouse genome (mm10) using HISAT2.

The aligned SAM/BAM files of each human samples are performed gene expression analysis in TPM value by StringTie and merged the gene abundance files into one tab-delimited file using linux commands for downstream statistical analysis.

The orginial XenofilteR source code is available at https://github.com/PeeperLab/XenofilteR

Raw paired-end Fastq files are aligned to human reference genome using Partek (version) then apply XenofileR to distinguish the human and mouse reads in patient derived xenograft sequencing data.