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 3 months ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 7 months ago
• nf-core / pathogensurveillance
  Surveillance of pathogens using population genomics and sequencing
  ☆22Updated last week
• pmenzel / taxonomy-tools
  C++ tools for NCBI taxonomy tasks
  ☆11Updated 3 years ago
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 6 years ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• aesheppard / TETyper
  transposable element typing pipeline
  ☆17Updated last year
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated 10 months ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 4 months ago
• mmpust / raspir
  Raspir, the rare species identifier
  ☆11Updated last year
• FredHutch / nf-anvio-pangenome
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆17Updated last year
• smangul1 / MiCoP
  MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
  ☆15Updated 3 years ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 4 months ago
• SR-Martin / alvis
  ☆19Updated last year
• 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
• oxli-bio / oxli
  k-mers and the like
  ☆21Updated this week
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆19Updated 2 months ago
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• bo1929 / krepp
  A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.
  ☆10Updated this week
• AllTheBacteria / Phylign
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12Updated 11 months ago
• TGenNorth / NASP
  Northern Arizona SNP Pipeline
  ☆19Updated 5 months ago
• scwatts / genome_painter
  Paint genomes with taxa-specific k-mer probabilities
  ☆15Updated 3 years ago
• SWIAI / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated last year
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 3 months ago
• quadram-institute-bioscience / dadaist2
  Dadaist2 🟨 Highway to R
  ☆13Updated last month
• ctb / 2025-ncbi-rest-api
  Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t
  ☆11Updated 2 months ago
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 2 years ago
• farhat-lab / fast-lineage-caller
  ☆14Updated 3 years ago
• sid-krish / rhometa
  metagenome population recombination rate estimation pipeline
  ☆12Updated 2 weeks ago