Alternatives and similar repositories for kallisto

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

• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆763Updated 2 weeks ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆747Updated 4 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆456Updated last year
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆851Updated last year
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆426Updated last week
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆533Updated 3 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆533Updated 5 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 3 months ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆311Updated 6 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆499Updated 5 years ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,013Updated 9 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆851Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆438Updated 4 months ago
• hbctraining / DGE_workshop
  ☆403Updated 3 years ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆557Updated 2 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆348Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆856Updated 6 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆527Updated this week
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆591Updated last year
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆877Updated 10 months ago
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆832Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,397Updated this week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆755Updated 2 weeks ago
• marcelm / cutadapt
  Cutadapt removes adapter sequences from sequencing reads
  ☆566Updated last week
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,163Updated last week
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,515Updated 6 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆472Updated 3 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆513Updated last week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆677Updated 5 months ago