Alternatives and similar repositories for AGAT:

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

• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆209Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆285Updated 5 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆581Updated last week
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆338Updated 2 weeks ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆495Updated last year
• usadellab / Trimmomatic
  ☆238Updated 9 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated last week
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆472Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆264Updated last year
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆596Updated 10 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆421Updated this week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆221Updated 4 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆354Updated 2 years ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆399Updated last week
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆400Updated 2 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆492Updated last week
• 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…
  ☆391Updated 2 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆194Updated last month
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆586Updated this week
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆463Updated last month
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆316Updated 9 months ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆353Updated 10 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆210Updated last week
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆382Updated 10 months ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆307Updated last year
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆257Updated 2 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆288Updated last year
• kcleal / gw
  Genome browser and variant annotation
  ☆296Updated last month
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆339Updated 7 months ago