Alternatives and similar repositories for squirrel

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

• quick-lab / SARS-CoV-2
  SARs-CoV-2 Primer schemes
  ☆16Updated 2 months ago
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆38Updated 3 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 3 months ago
• iqtree / piqtree
  A Python library that exposes features from IQ-TREE - efficient software for phylogenomic inference
  ☆31Updated last week
• rpetit3 / fastq-scan
  Output FASTQ summary statistics in JSON format
  ☆30Updated 2 years ago
• enasequence / webin-cli
  Webin command line submission program.
  ☆33Updated this week
• KatyBrown / plot_phylo
  Python package to plot a phylogenetic tree on an existing matplotlib axis.
  ☆23Updated this week
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆40Updated 8 months ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆52Updated 3 months ago
• MDU-PHL / pango-collapse
  app to collapse Pango lineages for reporting
  ☆13Updated last year
• ncbi / sra-human-scrubber
  An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…
  ☆49Updated this week
• jonas-fuchs / varVAMP
  Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
  ☆41Updated last month
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆36Updated 3 years ago
• rpetit3 / vcf-annotator
  Add biological annotations to variants in a given VCF file.
  ☆32Updated 3 years ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆35Updated last month
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆38Updated last month
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 4 months ago
• LuoGroup2023 / PanTax
  PanTax: Strain-level metagenomic profiling using pangenome graphs
  ☆39Updated this week
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• bcgsc / LongStitch
  🪡Correct and scaffold assemblies using long reads
  ☆55Updated last year
• rrwick / Verticall
  Recombination-free trees
  ☆58Updated 4 months ago
• nextgenusfs / funannotate2
  Eukaryotic genome annotation software.
  ☆18Updated this week
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆44Updated last month
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆28Updated last week
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆32Updated 7 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• dhelekal / CaveDive
  ☆17Updated last year
• GuyBaele / SpreadGL
  Main development repository for SpreadGL
  ☆18Updated 9 months ago
• dib-lab / genome-grist
  map Illumina metagenomes to genomes!
  ☆39Updated 2 weeks ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated last year