Alternatives and similar repositories for sam2lca

Users that are interested in sam2lca are comparing it to the libraries listed below

• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated 4 months ago
• FredHutch / nf-anvio-pangenome
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆17Updated last year
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 8 months ago
• pmenzel / taxonomy-tools
  C++ tools for NCBI taxonomy tasks
  ☆11Updated 3 years ago
• SwingOlive / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated last year
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 weeks ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆24Updated this week
• mmpust / raspir
  Raspir, the rare species identifier
  ☆11Updated last year
• smangul1 / MiCoP
  MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
  ☆15Updated 3 years ago
• ewissel / hAMRoaster
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Updated last year
• maxemil / PhyloMagnet
  screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics
  ☆11Updated 4 years ago
• quadram-institute-bioscience / dadaist2
  Dadaist2 🟨 Highway to R
  ☆13Updated 3 months ago
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated 11 months ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 6 months ago
• salzberg-lab / bolotie
  SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
  ☆13Updated last year
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 6 months ago
• aesheppard / TETyper
  transposable element typing pipeline
  ☆18Updated last year
• janepipistrelle / bacterial_GWAS_tutorial
  Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
  ☆18Updated 9 years ago
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆19Updated 4 months ago
• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆27Updated 3 weeks ago
• farhat-lab / fast-lineage-caller
  ☆14Updated 3 years ago
• SR-Martin / alvis
  ☆20Updated last year
• katholt / AMRrules
  Organism-specific interpretation of AMR genotypes
  ☆12Updated last year
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆23Updated 2 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• dhelekal / CaveDive
  ☆17Updated 11 months ago
• Adamtaranto / blast-besties
  Rapid discovery of reciprocal best blast pairs.
  ☆10Updated 6 months ago