Alternatives and similar repositories for spades

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

• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆942Updated last year
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆883Updated 7 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆853Updated 2 weeks ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆819Updated 4 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆677Updated 5 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆628Updated last year
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆755Updated 2 weeks ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆798Updated last month
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆695Updated 3 weeks ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆710Updated 8 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆557Updated 2 weeks ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆878Updated last week
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆654Updated 3 years ago
• ablab / quast
  Genome assembly evaluation tool
  ☆485Updated last year
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,051Updated 4 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆571Updated last week
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆623Updated last year
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆460Updated this week
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆551Updated 4 months ago
• mummer4 / mummer
  Mummer alignment tool
  ☆539Updated 10 months ago
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆517Updated last week
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆555Updated last year
• nanoporetech / dorado
  Oxford Nanopore's Basecaller
  ☆765Updated 3 weeks ago
• hyattpd / Prodigal
  Prodigal Gene Prediction Software
  ☆519Updated last year
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆877Updated 10 months ago
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆487Updated 3 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 3 months ago
• ComparativeGenomicsToolkit / cactus
  Official home of genome aligner based upon notion of Cactus graphs
  ☆630Updated last week
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,515Updated 6 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆543Updated last year