indel

There are 0 repository under indel topic.

• ShixiangWang / sigminer

  🌲 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

  mutational-signaturescopynumber-signaturessomatic-variantssomatic-mutationscosmic-signaturessignature-extractionnmfnmf-extractionbayesian-nmfbioinformaticsrcancer-researchvisualizationsbsdbsindelcnveasy-to-use
  Language:R 137

• gear-genomics / tracy

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

  chromatogrampcrtracysanger-trace-alignmentsanger-sequencingsequencingvariant-callingalignmentgenetic-engineeringpcr-productscrispr-cas9crispr-analysisindelindel-discoverysanger-chromatograms
  Language:C++ 96

• orangeSi / GSSplayground

  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, directly modify almost all features in Chrome by click the feature

  genomesgeneclustersyntenycrosslinkbioinformaticssvgvcfsnpbamread-mappingdepthvisualizationstructure-variationgenome-viewersvtranscriptomicsigv-likecomparative-genomicslong-readsindel
  Language:HTML 31

• stjude / indelPost

  Python library for simple and complex indels.

  indelbioinformaticsphasingrealignmentgenotyping
  Language:C 12
• acorn

  TNTurnerLab / acorn

  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.

  denovogenomegenomicsindelmnvrsnvvariants
  Language:R 6

• nickveltmaat / SNVcaller

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

  cell-free-dnacfdnactdnaindellofreqmutect2sinvictsnvsnv-annotationsnvssomatic-mutationssomatic-variantsvardict
  Language:Python 3

• xjtu-omics / ChineseQuartetGenome

  Genome assembly and variant benchmarks for Chinese Quartet

  genome-assemblychinese-quartetvariant-benchmarkindelsnvhaplotype-resolved-assemblystructural-variants
  Language:Python 3

• Computational-Genomics-BSC / plink-bed-reader

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

  bedbioinformaticsgeneticsgenotypeindelplinksnvvariant
  Language:Python 1

• EUCANCan / prepy-wrapper

  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.

  genomicsindelsnvvariantsvcf
  Language:Python 1

• Sydney-Informatics-Hub / GermlineShortV_biovalidation

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

  germlineindelsnpvalidationvariant-analysisvariant-callingwgswholegenomesequencing
  Language:Shell