Alternatives and similar repositories for stringtie

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

• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆419Updated 5 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆291Updated 8 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆471Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆424Updated 2 months ago
• usadellab / Trimmomatic
  ☆253Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆596Updated 2 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 11 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆271Updated 5 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆509Updated this week
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆511Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆262Updated last month
• pcingola / SnpEff
  ☆279Updated 4 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆482Updated last month
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated last year
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆212Updated 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…
  ☆411Updated 5 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆242Updated 2 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆227Updated this week
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆229Updated last month
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆234Updated 4 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆215Updated 2 months ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆388Updated last year
• Xinglab / rmats-turbo
  ☆263Updated 7 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆138Updated 10 years ago
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆486Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆297Updated 2 years ago