PALMER
February 9, 2026 ยท View on GitHub
PALMER detects non-reference mobile element insertions (LINE, Alu, SVA, HERVK) and other insertions (for example, NUMTs and HPV) from long-read sequencing and assembled contigs.
Documentation
- The most recent version is 2.3.3. See Changelog
Full documentation is in the wiki:
Issues
Quick Build
git clone https://github.com/WeichenZhou/PALMER.git
cd PALMER
make
Note: install htslib development headers and ncbi-blast++/2.10.0 before building.
Citation
For PALMER /* where it begins (Pre-mAsking Long reads for Mobile Element inseRtion) */:
- Weichen Zhou et al., Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology, Nucleic Acids Research, 2019, gkz1173,
https://doi.org/10.1093/nar/gkz1173
For TEnCATS/NanoPal:
- Torrin L. McDonald and Weichen Zhou et al., Cas9 targeted enrichment of mobile elements using nanopore sequencing, Nature Communications, 2021,
https://doi.org/10.1038/s41467-021-23918-y
For PALMER2.0 multi-functional usage in WGS, capture, assembled contigs, and single-cell data:
- Weichen Zhou et al., A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex, bioRxiv, 2024,
https://doi.org/10.1101/2024.12.18.629274
For SMaHT benchmarking:
- Wang et al., Multi-platform framework for mapping somatic retrotransposition in human tissues, bioRxiv, 2025,
https://doi.org/10.1101/2025.10.07.680917
Contact
Copyright
Copyright (c) 2018-2026 Weichen Arthur Zhou @ UMich&Fudan&HUST