Alternatives and similar repositories for jcvi:

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

• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆588Updated 9 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆738Updated 3 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆808Updated 5 months ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆332Updated 2 years ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆576Updated 2 weeks ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆487Updated 3 weeks ago
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆513Updated last week
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆793Updated 7 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆489Updated last year
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆478Updated this week
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆393Updated last week
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆413Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆697Updated this week
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆864Updated 10 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆495Updated 3 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆412Updated this week
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆370Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆406Updated last month
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆735Updated 6 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆576Updated last week
• ablab / quast
  Genome assembly evaluation tool
  ☆422Updated 3 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆582Updated 6 months ago
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆553Updated 2 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆462Updated 4 years ago
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆493Updated 7 months ago
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆436Updated 4 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆285Updated 4 months ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆348Updated 9 months ago
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆355Updated 6 months ago
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆377Updated 3 weeks ago