🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, dire…

Python library for simple and complex indels.

acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

Genome assembly and variant benchmarks for Chinese Quartet

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in pure Python.

Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis.

Workflow for biological validation of germline SNP and indel variant datasets.