Research graph
References from HaploCharmer: a Snakemake workflow for read-scale haplotype calling adapted to polyploids. Local targets link to admitted publications; unresolved targets remain external evidence.
HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data
10.1089/cmb.2012.0084 · 2012 · External reference
Haplotype assembly in polyploid genomes and identical by descent shared tracts
10.1093/bioinformatics/btt213 · 2013 · External reference
Features and applications of haplotypes in crop breeding
10.1038/s42003-021-02782-y · 2021 · External reference
Haplotype calling in complex polyploids using a single streamlined workflow
10.24072/pci.genomics.100434 · 2025 · External reference
Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
10.1101/gr.1917404 · 2004 · External reference
Haplotype-Based Genotyping in Polyploids
10.3389/fpls.2018.00564 · 2018 · External reference
Twelve years of SAMtools and BCFtools
10.1093/gigascience/giab008 · 2021 · External reference
A framework for variation discovery and genotyping using next-generation DNA sequencing data
10.1038/ng.806 · 2011 · External reference
Maximum Likelihood from Incomplete Data Via the EM Algorithm
10.1111/j.2517-6161.1977.tb01600.x · 1977 · External reference
Unveiling the predominance of Saccharum spontaneum alleles for resistance to orange rust in sugarcane using genome-wide association
10.1007/s00122-024-04583-3 · 2024 · External reference
Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics
10.1007/bf02174028 · 1996 · External reference
A mosaic monoploid reference sequence for the highly complex genome of sugarcane
10.1038/s41467-018-05051-5 · 2018 · External reference
Combining Markers into Haplotypes Can Improve Population Structure Inference
10.1534/genetics.111.131136 · 2012 · External reference
Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe
10.1038/hdy.1994.148 · 1994 · External reference
RFLP Mapping in Cultivated Sugarcane (Saccharum spp.): Genome Organization in a Highly Polyploid and Aneuploid Interspecific Hybrid
10.1093/genetics/142.3.987 · 1996 · External reference
Efficient algorithms for polyploid haplotype phasing
10.1186/s12864-018-4464-9 · 2018 · External reference
The complex polyploid genome architecture of sugarcane
10.1038/s41586-024-07231-4 · 2024 · External reference
Snakemake—a scalable bioinformatics workflow engine
10.1093/bioinformatics/bts480 · 2012 · External reference
OneMap: software for genetic mapping in outcrossing species: OneMap
10.1111/j.2007.0018-0661.02000.x · 2007 · External reference
Ranbow: A fast and accurate method for polyploid haplotype reconstruction
10.1371/journal.pcbi.1007843 · 2020 · External reference
Sustainable data analysis with Snakemake
10.12688/f1000research.29032.2 · 2021 · External reference
Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane
10.1007/s00438-010-0546-3 · 2010 · External reference
Sugarcane genome architecture decrypted with chromosome‐specific oligo probes
10.1111/tpj.14881 · 2020 · External reference
HaploCharmer supplementary figures and codes
10.5281/zenodo.17185943 · 2025 · External reference
Efficient “pythonic” access to FASTA files using pyfaidx
10.7287/peerj.preprints.970v1 · 2015 · External reference
PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data
10.1186/s12859-022-04989-0 · 2022 · External reference
Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’ crop with ‘bitter’ genomes
10.1111/pbi.12992 · 2018 · External reference