Alternatives and similar repositories for gffutils:

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

• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated 3 weeks ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆214Updated 8 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆287Updated 6 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆210Updated last year
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆237Updated last year
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆197Updated last week
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆354Updated 2 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆239Updated 11 months ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆124Updated 4 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated last month
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆133Updated 10 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆249Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆539Updated 8 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆224Updated 4 years ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 5 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆248Updated 9 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆402Updated 3 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆258Updated 3 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆213Updated last week
• broadinstitute / viral-ngs
  Viral genomics analysis pipelines
  ☆192Updated 6 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆319Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆136Updated 3 years ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆376Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆145Updated last year
• barricklab / breseq
  breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is inte…
  ☆159Updated 2 weeks ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆207Updated last year
• 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…
  ☆297Updated last year