Table 1 Overview of the tools benchmarked in this study
From: Benchmarking mouse contamination removing protocols in patient-derived xenografts genomic profiling
Protocols | Input | Aligner | Output | Algorithm | Language | Release |
|---|---|---|---|---|---|---|
Disambiguate | BAM, name sorted | STAR, HISAT, BWA | BAM | Mapping score and quality | Python, C + + | 2016 |
Bamcmp | BAM, name sorted | STAR, HISAT, BWA | BAM | Mapping score and quality | C + + | 2017 |
XenofilteR | BAM, coordinate sorted | STAR, HISAT, BWA | BAM | Mapping score and quality | R | 2018 |
Xenome | Fastq | NA | Fastq | K-mer | C + + | 2012 |
BBSplit | Fastq | BBMAP | Fastq | K-mer | Java | 2020 |
Xengsort | Fastq | NA | Fastq | K-mer | Python, numba | 2021 |
