C++ library and cmdline tools for parsing and manipulating VCF files
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May 1, 2022 - C++
#
genotyping
Here are 41 public repositories matching this topic...
Graph realignment tools for structural variants
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Updated
Mar 9, 2022 - C++
public-health
report
variant-calling
bacteria
fastq
phylogenomics
denovo-assembly
genotyping
resistome
virulome
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Updated
Aug 3, 2020 - Perl
A method for variant graph genotyping based on exact alignment of k-mers
ngs
bayesian-inference
variant-calling
indels
gibbs-sampling
structural-variation
snvs
dna-sequencing
genotyping
k-mers
variant-graphs
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Updated
Apr 1, 2019 - C++
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
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May 22, 2021 - Python
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
ngs
circrna
structural-variation
circrna-prediction
genotyping
circrnas
eccdna
ecdna
circular-dna
microdna
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Updated
Mar 10, 2021 - Python
Efficient genotyping bi-allelic SNPs on single cells
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Updated
Nov 3, 2021 - C
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
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Updated
Feb 10, 2019 - C++
Genotyping of segregating mobile elements insertions
bioinformatics
vcf
alu
transposons
transposable-elements
genotype-likelihoods
genotyping
short-reads
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Jul 29, 2021 - Perl
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Updated
Mar 7, 2021 - Forth
Toolkit for VNTR genotyping and repeat-pan genome graph construction
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Updated
Apr 1, 2022 - C++
Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
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Updated
Apr 14, 2022 - Python
A simple python library to identify the most likely strain from the population
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Updated
Feb 18, 2022 - Python
An efficient genetic data imputation pipeline
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Updated
Apr 7, 2022 - R
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
numpy
array
haplotypes
bayesian-inference
dna-sequences
genotyping
polyploidy
haplotype-assembly
haplotype-blocks
polyploid-genotyping
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Updated
Apr 8, 2022 - Python
genotyping by Mapping-free ALternate-allele detection of known VAriants
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Updated
Mar 24, 2022 - C
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
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Updated
Sep 25, 2020 - Python
Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences
virus
recombination
subtyping
genotyping
kmers
ancestral-sequences
phylo-kmers
recombination-detection
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Updated
Jan 12, 2021 - C++
emm Automatic Isolate Labeller
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Apr 27, 2022 - Jupyter Notebook
Visualisation application for Klebsiella genotypes generated by Kleborate.
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Mar 8, 2021 - R
One-step genotyping software using a long-read sequencer
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Mar 22, 2022 - Python
Microsatellite genotyping
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Nov 16, 2021 - Python
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
bioinformatics
snakemake
stack
genomics
singularity
vcf
snp
variant-calling
population-genetics
fastq
gbs
radseq
demultiplexing
genotyping
ddocent
singularity-recipe
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Updated
Aug 20, 2019 - Shell
Benchmarking variant callers for long read data
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Updated
Jun 28, 2021 - Python
R 📦 providing classes and functions to simulate breeding schemes.
r
simulation
breeding
phenotyping
phenotype
r-package
genetic
genotyping
diot
iwata
simulate-breeding-schemes
genotypic-data
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Updated
Oct 25, 2021 - R
A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)
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Nov 16, 2021 - JavaScript
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Nov 12, 2021 - wdl
Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results
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Aug 12, 2021 - Python
Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.
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Aug 29, 2021 - Python
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