Alternatives and similar repositories for dnaapler

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

• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆141Updated last month
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆81Updated 5 months ago
• bede / hostile
  Precise host read removal
  ☆105Updated last month
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆81Updated last year
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆61Updated 7 months ago
• thanhleviet / ISfinder-sequences
  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…
  ☆70Updated 5 years ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated 2 years ago
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆99Updated 6 months ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆76Updated last week
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆48Updated 2 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆85Updated 5 months ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆49Updated last year
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆71Updated 5 months ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆81Updated 3 months ago
• Serka-M / mmlong2-lite
  Lightweight bioinformatics pipeline for microbial genome recovery
  ☆17Updated last week
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆51Updated this week
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 5 months ago
• Hydro3639 / NanoPhase
  Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …
  ☆32Updated last year
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆52Updated 10 months ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆49Updated last month
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆39Updated 4 months ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated 3 weeks ago
• Kirk3gaard / 2025-Crowdsource-GPU-basecalling-stats
  A repository for collecting GPU basecalling stats
  ☆64Updated 2 weeks ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated last month
• AnantharamanLab / vRhyme
  Binning Virus Genomes from Metagenomes
  ☆65Updated 3 years ago
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆73Updated 2 years ago