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
  ☆429Updated 8 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆522Updated 3 weeks ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆296Updated 10 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆431Updated 2 weeks ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆273Updated last year
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆498Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆523Updated 5 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆484Updated last week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆448Updated last year
• usadellab / Trimmomatic
  ☆263Updated last week
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆509Updated 9 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆612Updated this week
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆468Updated this week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆257Updated 2 years ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆418Updated last year
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆511Updated 2 weeks ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆273Updated last week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated this week
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆456Updated 9 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆344Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆236Updated this week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆374Updated 2 months ago
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆495Updated last week
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆527Updated last year
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆369Updated last year
• mummer4 / mummer
  Mummer alignment tool
  ☆525Updated 6 months ago