Alternatives and similar repositories for STAR

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

• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,365Updated 3 weeks ago
• OpenGene / fastp
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,192Updated 3 weeks ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆872Updated 8 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,498Updated 4 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆834Updated last year
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,109Updated 3 weeks ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆756Updated 2 months ago
• ncbi / sra-tools
  SRA Tools
  ☆1,261Updated this week
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆825Updated last year
• griffithlab / rnaseq_tutorial
  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…
  ☆1,387Updated 2 years ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,043Updated 3 years ago
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,016Updated last year
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆741Updated last month
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,660Updated 6 months ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,787Updated 2 weeks ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆702Updated 6 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆737Updated 2 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆785Updated 3 months ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆999Updated 6 months ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,131Updated 5 months ago
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,042Updated last month
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆843Updated last year
• bbuchfink / diamond
  Accelerated BLAST compatible local sequence aligner.
  ☆1,189Updated 3 weeks ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆797Updated 2 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆524Updated last month
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆858Updated last month
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,036Updated 2 months ago
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆935Updated last year
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆675Updated 3 years ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆513Updated last month