Alternatives and similar repositories for fieldbioinformatics

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

• connor-lab / ncov2019-artic-nf
  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…
  ☆91Updated last year
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆135Updated last year
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆127Updated last week
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆158Updated this week
• medvedevgroup / SibeliaZ
  A fast whole-genome aligner based on de Bruijn graphs
  ☆146Updated 3 months ago
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆105Updated 3 years ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆83Updated last week
• SorenKarst / longread_umi
  ☆78Updated 4 years ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆126Updated this week
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆80Updated 2 weeks ago
• tseemann / nullarbor
  "Reads to report" for public health and clinical microbiology
  ☆139Updated last year
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆119Updated last year
• ngs-fzb / MTBseq_source
  MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…
  ☆44Updated 9 months ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆171Updated 4 years ago
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆129Updated last month
• xiaochuanle / NECAT
  Nanopore data assembler
  ☆151Updated 3 years ago
• wdecoster / chopper
  ☆189Updated 3 weeks ago
• andersen-lab / ivar
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  ☆120Updated last week
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆159Updated 11 months ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated 11 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 8 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆164Updated last year
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆162Updated last year
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆137Updated 2 weeks ago
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆95Updated last month
• aresti / primalscheme
  a tool for designing primer panels for multiplex PCR.
  ☆102Updated last year
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆51Updated 3 weeks ago
• phac-nml / mob-suite
  MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  ☆146Updated last month
• CompSynBioLab-KoreaUniv / FunGAP
  FunGAP: fungal Genome Annotation Pipeline
  ☆111Updated last year