Alternatives and similar repositories for salmon

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

• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆720Updated 2 weeks ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆768Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆752Updated 6 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆541Updated last week
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,526Updated 8 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆525Updated last week
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆485Updated last month
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆537Updated 2 weeks ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆578Updated last month
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,417Updated 3 weeks ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆881Updated last year
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,021Updated 10 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,197Updated this week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆862Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆460Updated last year
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆862Updated last year
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆769Updated last week
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆442Updated 6 months ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆445Updated 2 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆816Updated 3 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆887Updated last month
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆536Updated last week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆530Updated this week
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆866Updated last week
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆829Updated 6 months ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆443Updated last month
• ncbi / sra-tools
  SRA Tools
  ☆1,300Updated this week
• marcelm / cutadapt
  Cutadapt removes adapter sequences from sequencing reads
  ☆570Updated 3 weeks ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆474Updated 5 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆507Updated 3 months ago