Alternatives and similar repositories for Bracken

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

• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆343Updated last year
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆324Updated last year
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆374Updated last week
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆299Updated 2 weeks ago
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆421Updated 9 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆246Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆234Updated 4 years ago
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆234Updated 2 years ago
• nf-core / mag
  Assembly and binning of metagenomes
  ☆239Updated this week
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆343Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆229Updated 2 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆242Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆426Updated last year
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆350Updated 3 years ago
• jiarong / VirSorter2
  customizable pipeline to identify viral sequences from (meta)genomic data
  ☆257Updated 6 months ago
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆214Updated 2 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆355Updated 3 weeks ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆527Updated 3 months ago
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆304Updated 3 months ago
• wwood / CoverM
  Read alignment statistics for metagenomics
  ☆348Updated 3 weeks ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆416Updated last week
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆271Updated 5 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆262Updated last month
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆207Updated last week
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆511Updated last year
• ParBLiSS / FastANI
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆411Updated last year
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆411Updated 5 months ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆387Updated last month
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆282Updated last month