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GitHub topics: genotype-frequency

deepomicslab/SpecHLA

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

Language: C++ - Size: 156 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 22 - Forks: 9

wshuai294/PStrain

Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for any species.

Language: Shell - Size: 98.4 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 8 - Forks: 2

Related Keywords
genotype-frequency 2 phase 2 strain 1 snp 1 profile-strains 1 microbial-strain 1 metaphlan3 1 metagenotyping 1 metagenomics-toolkit 1 marker-gene-analysis 1 reads-binning 1 pacbio-data 1 nanopore 1 loss-of-heterozygosity 1 loh 1 local-assembly 1 immunity 1 human-leukocyte-antigens 1 hla-typing 1 hla-sequence 1 haplotype 1 cancer 1 allelic-imbalance 1