Alternatives and similar repositories for gffutils

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

• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆215Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆272Updated 3 weeks ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆146Updated 10 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆242Updated 2 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆277Updated 8 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆277Updated last month
• TransDecoder / TransDecoder
  TransDecoder source
  ☆298Updated last week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆283Updated 11 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆275Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆351Updated 5 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆439Updated 9 months ago
• agordon / fastx_toolkit
  FASTA/FASTQ pre-processing programs
  ☆190Updated 3 years ago
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆224Updated 8 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆214Updated last year
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆223Updated 2 months ago
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆227Updated 3 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆552Updated last year
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆317Updated last month
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆216Updated last year
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated last week
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆270Updated 2 years ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆318Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆241Updated 4 years ago
• veg / hyphy
  HyPhy: Hypothesis testing using Phylogenies
  ☆242Updated this week
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆211Updated 3 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆321Updated 6 months ago
• whatshap / whatshap
  Read-based phasing of genomic variants, also called haplotype assembly
  ☆383Updated 3 months ago
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆181Updated 2 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆247Updated last year