Alternatives and similar repositories for fastq-scan

Users that are interested in fastq-scan are comparing it to the libraries listed below

• tseemann / seeka
  Get microbial sequence data easier and faster
  ☆28Updated 5 years ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆25Updated last year
• tseemann / berokka
  🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
  ☆25Updated 6 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 6 years ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆48Updated 2 years ago
• h3abionet / TADA
  TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region
  ☆22Updated this week
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆41Updated 2 months ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• sanger-pathogens / seroba
  k-mer based Pipeline to identify the Serotype from Illumina NGS reads
  ☆25Updated 2 years ago
• dib-lab / charcoal
  Remove contaminated contigs from genomes using k-mers and taxonomies.
  ☆59Updated last year
• mbhall88 / nohuman
  Remove human reads from a sequencing run
  ☆40Updated 2 months ago
• mbhall88 / tbpore
  Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
  ☆12Updated last year
• thackl / proovframe
  frame-shift correction for long-read (meta)genomics
  ☆33Updated last year
• mjsull / chromatiblock
  Colinear block visualisation tool
  ☆31Updated last year
• farhat-lab / fast-lineage-caller
  ☆14Updated 4 years ago
• theiagen / public_health_bacterial_genomics
  ☆26Updated 2 years ago
• EnzoAndree / FastMLST
  ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies
  ☆27Updated last week
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆38Updated 2 weeks ago
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆36Updated 5 years ago
• hzi-bifo / Haploflow
  ☆30Updated 2 years ago
• JensUweUlrich / Taxor
  Fast and space-efficient taxonomic classification of long reads
  ☆43Updated 2 months ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆24Updated 2 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆30Updated last month
• chrisruis / MutTui
  MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
  ☆29Updated last year
• OLC-Bioinformatics / ConFindr
  Intra-species bacterial contamination detection
  ☆25Updated 8 months ago
• esteinig / sketchy
  Genomic neighbor typing of bacterial pathogens using MinHash
  ☆43Updated 2 years ago
• bluenote-1577 / floria
  Strain-level haplotyping for metagenomes with short or long-reads.
  ☆55Updated 6 months ago
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆51Updated 4 years ago
• mbhall88 / lrge
  Genome size estimation from long read overlaps
  ☆62Updated last month
• nf-core / bactmap
  A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
  ☆59Updated last week