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 6 months ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆23Updated 10 months ago
• 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
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 8 months ago
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• phac-nml / neptune
  Neptune: Genomic Signature Discovery
  ☆20Updated 8 months ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• phiweger / uv
  Finding prophage regions in bacterial genomes using brute force
  ☆22Updated 2 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
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆11Updated last year
• pmenzel / taxonomy-tools
  C++ tools for NCBI taxonomy tasks
  ☆11Updated last month
• CAMI-challenge / CAMITAX
  CAMITAX: Taxon labels for microbial genomes
  ☆30Updated last year
• althonos / pyskani
  PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
  ☆27Updated 2 weeks ago
• katholt / reddog-nf
  pipeline for read mapping, snp calling and annotation for bacterial genomes
  ☆12Updated last year
• bo1929 / krepp
  A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.
  ☆12Updated 3 weeks ago
• SR-Martin / alvis
  ☆20Updated last year
• phiweger / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆15Updated 7 years ago
• lskatz / SneakerNet
  QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run
  ☆11Updated 8 months ago
• salzberg-lab / bolotie
  SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
  ☆13Updated last year
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆27Updated 5 months ago
• quadram-institute-bioscience / dadaist2
  Dadaist2 🟨 Highway to R
  ☆13Updated 5 months ago
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 2 months ago
• moshi4 / plot_genome_align_fig
  Plot genome alignment figure using progressiveMauve & genoPlotR
  ☆22Updated 3 years ago
• AfZheng126 / MORA
  MetagenOmic read Re-Assigner and abundance quantifier
  ☆19Updated 6 months ago
• pirovc / grimer
  GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…
  ☆23Updated 2 years ago
• genomic-medicine-sweden / gms_16S
  A pipeline based on EMU, a taxonomic profiler optimized for long 16S rRNA reads.
  ☆14Updated last week
• esteinig / vircov
  Viral genome coverage evaluation for metagenomic diagnostics
  ☆28Updated 7 months ago
• FredHutch / nf-anvio-pangenome
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆17Updated last year