Alternatives and similar repositories for haploclique

Users that are interested in haploclique are comparing it to the libraries listed below

• cbg-ethz / ConsensusFixer

  View on GitHub
  Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.
  ☆18May 14, 2018Updated 7 years ago
• kuleshov / ProbHap

  View on GitHub
  Probabilistic single-individual haplotyping
  ☆10Mar 15, 2019Updated 6 years ago
• cbg-ethz / QuasiRecomb

  View on GitHub
  Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).
  ☆20May 3, 2017Updated 8 years ago
• CFSAN-Biostatistics / snp-mutator

  View on GitHub
  Generate mutated sequence files from a reference genome.
  ☆11Dec 26, 2022Updated 3 years ago
• cbg-ethz / shorah

  View on GitHub
  Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
  ☆41Feb 24, 2023Updated 2 years ago
• sinamajidian / phaseme

  View on GitHub
  A tool set to assess the quality of the per read phasing and reduce the errors.
  ☆13Jun 25, 2020Updated 5 years ago
• ProSolo / prosolo

  View on GitHub
  ProSolo, variant calling from single cell DNA-seq data, or: bulk backing vocals for single cell solos.
  ☆21Sep 1, 2021Updated 4 years ago
• cbg-ethz / ngshmmalign

  View on GitHub
  ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and H…
  ☆10May 3, 2018Updated 7 years ago
• sapporo-wes / sapporo-service

  View on GitHub
  A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specific…
  ☆24Jan 21, 2026Updated 3 weeks ago
• sanger-pathogens / saffrontree

  View on GitHub
  SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
  ☆25Jun 11, 2020Updated 5 years ago
• ywchoi / phasing

  View on GitHub
  Evaluation of phasing performance
  ☆23Mar 6, 2018Updated 7 years ago
• igvteam / igv.js-flask

  View on GitHub
  Example project for integrating igv.js and flask
  ☆26May 17, 2025Updated 8 months ago
• bede / kindel

  View on GitHub
  Indel-aware consensus for aligned BAM
  ☆21Aug 16, 2025Updated 6 months ago
• ryhui / imputation-pipeline

  View on GitHub
  ☆11Jun 26, 2020Updated 5 years ago
• deepomicslab / SpecHap

  View on GitHub
  ☆12Dec 6, 2023Updated 2 years ago
• shilpagarg / WHdenovo

  View on GitHub
  ☆46Jun 21, 2020Updated 5 years ago
• btmartin721 / raxml_ascbias

  View on GitHub
  Script for removing or counting invariant sites for the RAxML ascertainment bias corrections
  ☆16Oct 12, 2024Updated last year
• PacificBiosciences / pbmarkdup

  View on GitHub
  Mark duplicate reads from PacBio sequencing of an amplified library
  ☆12Feb 26, 2025Updated 11 months ago
• GATB / bloocoo

  View on GitHub
  Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint.
  ☆12May 22, 2017Updated 8 years ago
• SciLifeLab / NGI-MethylSeq

  View on GitHub
  This pipeline has moved! Please see:
  ☆11Mar 12, 2018Updated 7 years ago
• LeilyR / Multi-genome-Reference

  View on GitHub
  A program to generate a graph which presents a simplified representation of several full length genomes
  ☆13Aug 23, 2018Updated 7 years ago
• aquaskyline / 16GT

  View on GitHub
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Dec 26, 2023Updated 2 years ago
• shenwei356 / ncbi_acc2gtdb_acc

  View on GitHub
  Mapping NCBI Genbank accession to GTDB accession
  ☆14Feb 13, 2021Updated 5 years ago
• FredHutch / nf-anvio-pangenome

  View on GitHub
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆16Oct 11, 2023Updated 2 years ago
• MaikeMorrison / FSTruct

  View on GitHub
  ☆13Aug 18, 2023Updated 2 years ago
• lh3 / lh3-snippets

  View on GitHub
  ☆13Jan 23, 2020Updated 6 years ago
• VCCRI / dv-trio

  View on GitHub
  dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCF…
  ☆11Feb 3, 2021Updated 5 years ago
• collaborativebioinformatics / GeneVar

  View on GitHub
  ☆12Oct 13, 2021Updated 4 years ago
• melisaolave / SNPs2CF

  View on GitHub
  An R function to compute Concordance Factors from SNP datasets
  ☆15Dec 4, 2025Updated 2 months ago
• nf-core / vipr

  View on GitHub
  Assembly and intrahost / low-frequency variant calling for viral samples
  ☆15Feb 12, 2020Updated 6 years ago
• ThomasDOtto / ILRA

  View on GitHub
  Improvement of Long Read Assemblies (ILRA) is a pipeline to help in the post assembly process (finishing) by cleaning and merging contigs…
  ☆13Nov 9, 2024Updated last year
• davidemms / STAG

  View on GitHub
  STAG: Species Tree from All Genes
  ☆35Dec 10, 2018Updated 7 years ago
• DecodeGenetics / read_haps

  View on GitHub
  Detects human contamination in bam files
  ☆16Sep 10, 2020Updated 5 years ago
• edawson / svaha

  View on GitHub
  Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
  ☆11Mar 6, 2024Updated last year
• broadinstitute / gnomad-mitochondria

  View on GitHub
  ☆15Apr 10, 2024Updated last year
• NCBI-Hackathons / FlowBio

  View on GitHub
  A fast, easy way to present complex bioinformatics pipelines to biologists
  ☆11Sep 28, 2018Updated 7 years ago
• CMU-SAFARI / Scrooge

  View on GitHub
  Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…
  ☆38Jun 23, 2023Updated 2 years ago
• pangenome / maffer

  View on GitHub
  extract MSAs from genome variation graphs
  ☆34Sep 20, 2020Updated 5 years ago
• TGenNorth / NASP

  View on GitHub
  Northern Arizona SNP Pipeline
  ☆20Oct 29, 2024Updated last year