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C++ library and cmdline tools for parsing and manipulating VCF files
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Jul 29, 2020 - C++
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variant-calling
Here are 123 public repositories matching this topic...
Python library to facilitate genome assembly, annotation and comparative genomics
bioinformatics
genomics
comparative-genomics
variant-calling
sequence-alignments
genome-sequencing
genetic-maps
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Sep 4, 2020 - Python
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Aug 3, 2020 - Perl
A tool set for short variant discovery in genetic sequence data.
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Mar 31, 2020 - C
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
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Feb 13, 2020 - Python
Viral genomics analysis pipelines
genomics
genome
variant-calling
bam
genome-sequencing
illumina
fastq
genome-assembly
variant-annotations
viral-ngs
viral
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May 20, 2020 - Python
Bayesian haplotype-based mutation calling
bioinformatics
genomics
somatic-variants
haplotypes
variants
variant-calling
single-cell
phasing
de-novo-mutation
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Sep 6, 2020 - C++
De novo genome assembly and multisample variant calling
genomics
variant-calling
kmer
cortex
genome-analysis
genome-assembly
de-bruijn-graphs
genome-graph
contigs
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Mar 28, 2019 - C
De novo assembly based variant calling pipeline for Illumina short reads
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Dec 20, 2017 - TeX
Graph realignment tools for structural variants
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Sep 24, 2019 - C++
PacBio® variant and consensus caller
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Apr 25, 2019 - Python
public-health
report
variant-calling
bacteria
fastq
phylogenomics
denovo-assembly
genotyping
resistome
virulome
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Aug 3, 2020 - Perl
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
docker
workflow
bioinformatics
pipeline
genomics
nextflow
cancer
reproducible-research
containers
conda
next-generation-sequencing
singularity
reproducible-science
variant-calling
somatic
germline
nf-core
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Sep 4, 2020 - Nextflow
xHLA: Fast and accurate HLA typing from short read sequence data
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Oct 11, 2018 - Jupyter Notebook
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Sep 4, 2020 - Python
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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Apr 1, 2019 - C++
Genome inference from a population reference graph
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Aug 12, 2020 - C++
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
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Sep 4, 2020 - Python
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
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Jul 30, 2020
GATK RNA-Seq Variant Calling in Nextflow
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Aug 10, 2020 - Nextflow
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
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Jan 18, 2019 - C++
find large indels (in the blind spot between GATK/freebayes and SV callers)
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Dec 3, 2017 - Nim
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Jun 24, 2020 - TeX
Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.
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Sep 5, 2020 - C++
Reference-free variant discovery in large eukaryotic genomes
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Nov 22, 2019 - Python
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
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Sep 2, 2020 - C++
moldach
commented
Mar 20, 2020
I'm getting an error when trying to pull with singularity (version 3.5.2-1.el7)
singularity pull --name nf-core-deepvariant.simg shub://nf-core/deepvariant
FATAL: While pulling shub image: failed to get manifest for: shub://nf-core/deepvariant: the requested manifest was not found in singularity hub
Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files
sequencing
alignment
crispr-analysis
variant-calling
pcr
tracy
crispr-cas9
sanger-chromatograms
indel-discovery
chromatogram
sanger-trace-alignment
sanger-sequencing
pcr-products
genetic-engineering
indel
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Aug 8, 2020 - C++
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As we clean up and document the WDLs, it'll be good to have a graph/DAG visualization of workflows.
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