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
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated 2 months ago
• snayfach / MIDAS
  An integrated pipeline for estimating strain-level genomic variation from metagenomic data
  ☆128Updated last year
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆105Updated 3 years ago
• nanoporetech / ont-assembly-polish
  ONT assembly and Illumina polishing pipeline
  ☆89Updated 4 years ago
• mw55309 / Kraken_db_install_scripts
  Updated Kraken DB install scripts to cope with new-ish NCBI structure
  ☆47Updated 8 years ago
• SorenKarst / longread_umi
  ☆78Updated 4 years ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆98Updated last year
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆55Updated last year
• 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
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• rjchallis / assembly-stats
  Assembly statistic visualisation
  ☆90Updated last year
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆72Updated 3 years ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆57Updated 4 years ago
• MadsAlbertsen / multi-metagenome
  Scripts and tutorials on how to assemble individual microbial genomes from metagenomes
  ☆81Updated 9 years ago
• DiltheyLab / MetaMaps
  Long-read metagenomic analysis
  ☆103Updated last year
• BioInf-Wuerzburg / proovread
  PacBio hybrid error correction through iterative short read consensus
  ☆61Updated 6 years ago
• CSB5 / OPERA-MS
  OPERA-MS - Hybrid Metagenomic Assembler
  ☆95Updated last year
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• rhysf / Synima
  Synteny Imager
  ☆63Updated 10 months ago
• genotoul-bioinfo / dgenies
  Dotplot large Genomes in an Interactive, Efficient and Simple way
  ☆104Updated last week
• apetkau / orthomcl-pipeline
  Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/
  ☆80Updated 4 years ago
• khyox / recentrifuge
  Recentrifuge: robust comparative analysis and contamination removal for metagenomics
  ☆94Updated 2 months 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…
  ☆56Updated 3 years ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆105Updated 2 years ago
• BinPro / CONCOCT
  Clustering cONtigs with COverage and ComposiTion
  ☆131Updated 5 years ago
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆58Updated last year