Alternatives and similar repositories for treeseq-inference

Users that are interested in treeseq-inference are comparing it to the libraries listed below

• ramachandran-lab / SWIFr
  Sweep Inference Framework (controlling for correlation)
  ☆29Updated 10 months ago
• oscarlr / MsPAC
  Phase reads, assemble haplotypes and detect SVs
  ☆19Updated 4 years ago
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated last month
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆48Updated 3 years ago
• AgResearch / KGD
  Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment
  ☆21Updated 2 weeks ago
• jkbonfield / crumble
  Exploration of controlled loss of quality values for compressing CRAM files
  ☆34Updated 2 years ago
• tskit-dev / tsdate
  Infer the age of ancestral nodes in a tree sequence.
  ☆21Updated 2 months ago
• enormandeau / snplift
  Transfer coordinates across genomes
  ☆23Updated 2 weeks ago
• yangjl / GERP-diallel
  Research repo for Yang et al., 2017 paper.
  ☆9Updated 5 years ago
• lorinanthony / MAPIT
  Code and Tutorials for Running the MArginal ePIstasis Test (MAPIT)
  ☆15Updated 2 years ago
• myriad-opensource / samwell
  Samwell: a python package for using genomic files... well
  ☆20Updated 2 years ago
• slzarate / parliament2
  Runs a combination of tools to generate structural variant calls on short-read whole-genome sequencing data
  ☆21Updated 3 years ago
• ComparativeGenomicsToolkit / taffy
  This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
  ☆27Updated 5 months ago
• sanger-tol / genomeassembly
  Implementation of ToL genome assembly workflows
  ☆20Updated this week
• ywchoi / phasing
  Evaluation of phasing performance
  ☆23Updated 7 years ago
• ruolin / strawberry
  A program for fast and accurate genome-guided transcripts reconstruction and quantification from RNA-seq (Supporting Pacbio single-end)
  ☆23Updated 4 years ago
• cpockrandt / PhyloCSFpp
  PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…
  ☆31Updated 3 years ago
• bioinform / breakseq2
  BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants
  ☆24Updated 9 years ago
• jmonlong / sveval
  Functions to compare a SV call sets against a truth set.
  ☆29Updated last year
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆55Updated last year
• Gabaldonlab / haplotypo
  This is the Haplotypo repository
  ☆20Updated last year
• fritzsedlazeck / SVCollector
  Method to optimally select samples for validation and resequencing
  ☆27Updated 4 years ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated last year
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated 9 months ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆49Updated 5 years ago
• atifrahman / HAWK
  Hitting associations with k-mers
  ☆45Updated 3 years ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆42Updated last year
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• KiddLab / QuicK-mer2
  ☆11Updated 2 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆36Updated 11 months ago