Alternatives and similar repositories for gffread

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

• TransDecoder / TransDecoder
  TransDecoder source
  ☆289Updated 8 months ago
• usadellab / Trimmomatic
  ☆248Updated last year
• 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…
  ☆409Updated 4 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆230Updated 4 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆351Updated last week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆224Updated this week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆306Updated last month
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆224Updated 3 weeks ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆622Updated last year
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆508Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆266Updated last year
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆482Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆256Updated 3 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆267Updated 5 months ago
• pcingola / SnpEff
  ☆276Updated 3 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆212Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆439Updated 3 weeks ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆363Updated 3 years ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆212Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆330Updated 2 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆136Updated 10 years ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆514Updated 2 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆301Updated last year
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆252Updated 2 years ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆201Updated last week