Python library to facilitate genome assembly, annotation, and comparative genomics
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Updated
May 11, 2024 - Python
Python library to facilitate genome assembly, annotation, and comparative genomics
A Snakemake pipeline for variant calling of genomic FASTQ data using GATK
Long read production pipelines
Efficient variant-call data storage and retrieval library using the TileDB storage library.
A nextflow variant benchmarking pipeline - premature
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
vcfdist: Accurately benchmarking phased variant calls
This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ
Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Genomic Analysis Pipeline: Automate data preprocessing, variant calling, and annotation with Snakemake. Ensure reproducibility and reliability in genomic studies.
making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
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