Alternatives and similar repositories for angsd

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

• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆312Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆188Updated last year
• KamilSJaron / smudgeplot
  Inference of ploidy and heterozygosity structure using whole genome sequencing data
  ☆271Updated 2 weeks ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆213Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆229Updated 2 years ago
• schatzlab / genomescope
  Fast genome analysis from unassembled short reads
  ☆292Updated last year
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆206Updated 2 years ago
• popgenmethods / smcpp
  SMC++ infers population history from whole-genome sequence data.
  ☆168Updated last year
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆170Updated 2 years ago
• mahulchak / quickmerge
  A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
  ☆204Updated 2 years ago
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆203Updated last year
• VGP / vgp-assembly
  VGP repository for the genome assembly working group
  ☆193Updated last month
• millanek / Dsuite
  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
  ☆174Updated 6 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆262Updated last month
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆308Updated 2 months ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆390Updated last month
• jtlovell / GENESPACE
  ☆211Updated 5 months ago
• oushujun / LTR_retriever
  LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…
  ☆205Updated this week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆324Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆226Updated 5 months ago
• marcelauliano / MitoHiFi
  Find, circularise and annotate mitogenome from PacBio assemblies
  ☆183Updated last month
• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆192Updated 10 months ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆281Updated 8 months ago
• dfguan / purge_dups
  haplotypic duplication identification tool
  ☆247Updated last year
• ksamuk / pixy
  Software for painlessly estimating average nucleotide diversity within and between populations
  ☆136Updated last month
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆346Updated last year
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆365Updated 4 months ago
• isaacovercast / easySFS
  Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …
  ☆154Updated 10 months ago
• tangerzhang / ALLHiC
  ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
  ☆177Updated 8 months ago