Alternatives and similar repositories for surpi

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

• nanoporetech / qcat
  qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
  ☆80Updated 4 years ago
• nanoporetech / ont-assembly-polish
  ONT assembly and Illumina polishing pipeline
  ☆89Updated 5 years ago
• mw55309 / Kraken_db_install_scripts
  Updated Kraken DB install scripts to cope with new-ish NCBI structure
  ☆48Updated 8 years ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆108Updated last month
• SorenKarst / longread_umi
  ☆80Updated 5 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆76Updated 3 years ago
• rjchallis / assembly-stats
  Assembly statistic visualisation
  ☆91Updated last year
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆104Updated 4 years ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆102Updated last year
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• chasewnelson / SNPGenie
  Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
  ☆119Updated 2 years ago
• DiltheyLab / MetaMaps
  Long-read metagenomic analysis
  ☆107Updated 2 years ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• apetkau / orthomcl-pipeline
  Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
  ☆80Updated 5 years ago
• BioInf-Wuerzburg / proovread
  PacBio hybrid error correction through iterative short read consensus
  ☆60Updated 6 years ago
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆131Updated 2 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆57Updated last year
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆48Updated 6 years ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆57Updated 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…
  ☆42Updated 6 years ago
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆93Updated 2 weeks ago
• PacificBiosciences / pb-assembly
  PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
  ☆118Updated 5 years ago
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆116Updated last year
• glennhickey / progressiveCactus
  Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
  ☆88Updated 7 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…
  ☆58Updated 4 years ago
• dentearl / mafTools
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆109Updated 3 years ago
• CompSynBioLab-KoreaUniv / FunGAP
  FunGAP: fungal Genome Annotation Pipeline
  ☆111Updated 6 months ago