Alternatives and similar repositories for apples:

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

• HaploConduct / HaploConduct
  Haplotype-aware genome assembly toolkit
  ☆29Updated 5 years ago
• tlemane / kmdiff
  Differential k-mer analysis
  ☆36Updated last year
• balabanmetin / uDance
  ☆43Updated last year
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆31Updated 3 months ago
• JLSteenwyk / orthofisher
  a broadly applicable tool for automated gene identification and retrieval
  ☆31Updated 4 months ago
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆22Updated last week
• davidemms / SHOOT
  SHOOT.bio - the phylogenetic search engine
  ☆24Updated last year
• jermp / fulgor
  Fulgor is a fast and space-efficient colored de Bruijn graph index.
  ☆49Updated last week
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆31Updated 2 years ago
• IndexThePlanet / LoganSearch
  A k-mer search engine for all Sequence Read Archive public accessions
  ☆29Updated 5 months ago
• althonos / pyorthoani
  A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
  ☆25Updated last week
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆50Updated 2 weeks 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
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆36Updated last year
• HaploKit / vechat
  Correcting errors in noisy long reads using variation graphs
  ☆51Updated 2 years ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆52Updated last week
• marschall-lab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated last month
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆29Updated 3 weeks ago
• shahab-sarmashghi / Skmer
  Fast and accurate tool for estimating genomic distances between genome-skims
  ☆42Updated last year
• fpusan / SuperPang
  Non-redundant pangenome assemblies from multiple genomes or bins
  ☆13Updated 2 months ago
• mourisl / centrifuger
  Classifier for metagenomic sequences using FM-index with run-block compressed BWT.
  ☆56Updated this week
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 months ago
• dvdylus / read2tree
  ☆20Updated 3 years ago
• JensUweUlrich / ReadBouncer
  Fast and scalable nanopore adaptive sampling
  ☆33Updated last year
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆27Updated 4 months ago
• pierrepeterlongo / back_to_sequences
  ☆41Updated last month
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆26Updated 5 years ago
• rnajena / poseidon
  PoSeiDon: positive selection detection and recombination analysis pipeline
  ☆37Updated 2 months ago
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆21Updated last year