52 Open source projects that are alternatives of or similar to Snippy

cython + htslib == fast VCF and BCF processing

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

A Java API for high-throughput sequencing data (HTS) formats.

Toolset for SV simulation, comparison and filtering

Personal Cancer Genome Reporter (PCGR)

Syntax highlighting for computational biology

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

A collection of scripts and notes related to genomics and bioinformatics

Graph realignment tools for structural variants

Structural variant toolkit for VCFs

Bayesian genotyper for structural variants

vCard Serializer and Parser for C#

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Generic germline variant annotation pipeline

highly-efficient & lightweight mutation signature matrix aggregation

Scalable genomic data analysis.

C library for high-throughput sequencing data formats

This vCard PHP library can easily parse or generate/export vCards as .vcf

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

annotate a VCF with other VCFs/BEDs/tabixed files

VCF-kit: Assorted utilities for the variant call format

convert your 23andme raw file to VCF | DEPRECATED, please see https://github.com/plantimals/2vcf

Convert Telegram Contacts JSON File to VCF File

Home of the Genomic Feature and Variation Ontology (GFVO)

Genotyping of segregating mobile elements insertions

Python API for comprehensive GWAS analysis using GEMMA

Method to optimally select samples for validation and resequencing

Annotation of VCF variants with functional impact and from databases (executable+library)

A standalone and free application to explore genetics variations from VCF file

Genomic VCF to tab-separated values

Frequently used commands in bioinformatics

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Cancer Predisposition Sequencing Reporter (CPSR)

find large indels (in the blind spot between GATK/freebayes and SV callers)

tools for reading, writing, merging, and remapping SNPs

Powerful statistics for VCF files

Spark VCF data source implementation for Dataframes

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

calcardbackup: moved to https://codeberg.org/BernieO/calcardbackup

Learning the Variant Call Format

📊Evaluating, filtering, comparing, and visualising VCF

simple viewer for variant call format using htslib

A fluent builder class for vCard files.

vembrane filters VCF records using python expressions

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

🔧 Simple script in python to convert CSV files to VCF

Syntax highlighting for computational biology

A DNA Sequence Alignment/Map (SAM) library for Clojure

Haplotype VCF comparison tools