Alternatives and similar repositories for snp-pipeline

Users that are interested in snp-pipeline are comparing it to the libraries listed below

• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 4 years ago
• katholt / RedDog
  ☆36Updated 3 years ago
• metagenomics / denbi-nanopore-training
  de.NBI Nanopore Training Course
  ☆20Updated last month
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆60Updated 5 years ago
• Shamir-Lab / Recycler
  This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…
  ☆59Updated 4 years ago
• nanoporetech / ont_tutorial_basicqc
  A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt
  ☆30Updated 4 years ago
• marbl / harvest
  ☆53Updated 4 years ago
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆74Updated 8 years ago
• fanglab / mbin
  mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads
  ☆25Updated 2 years ago
• arq5x / nanopore-scripts
  Various scripts and recipes for working with nanopore data
  ☆34Updated 9 years ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆73Updated 9 months ago
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• snacktavish / TreeToReads
  Pipeline to generate NGS reads from a phylogeny
  ☆39Updated 2 years ago
• wdecoster / nanolyse
  Remove lambda phage reads from a fastq file
  ☆29Updated 2 years ago
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated last year
• tseemann / sixess
  🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
  ☆24Updated 7 years ago
• B-UMMI / long-read-catalog
  catalog for long-read sequencing tools
  ☆32Updated 2 years ago
• nanoporetech / pipeline-umi-amplicon
  Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers
  ☆33Updated last year
• jgurtowski / nanocorr
  Error correction for Oxford Nanopore data
  ☆47Updated 4 years ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆56Updated 4 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆40Updated 5 years ago
• mdcao / npScarf
  ☆26Updated 5 years ago
• blaxterlab / blobology
  Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …
  ☆46Updated 3 years ago
• chiulab / SURPI-plus-dist
  This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…
  ☆41Updated 5 years ago
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆37Updated 5 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• naturalis / wgs2ncbi
  Toolkit for preparing genomes for submission to NCBI
  ☆30Updated 3 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• cerebis / bin3C
  Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
  ☆23Updated 3 weeks ago
• cboursnell / crb-blast
  Conditional Reciprocal Best Blast
  ☆41Updated 8 years ago