Alternatives and similar repositories for TrimGalore

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

• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆422Updated last month
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆622Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆444Updated this week
• usadellab / Trimmomatic
  ☆248Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆721Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 2 weeks ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆295Updated 2 years ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆306Updated 2 years ago
• hbctraining / Intro-to-DGE
  ☆197Updated 2 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆811Updated 10 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆743Updated last month
• hbctraining / DGE_workshop
  ☆392Updated 3 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆413Updated 5 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆387Updated 5 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆230Updated 4 years ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆406Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆289Updated 7 months ago
• Xinglab / rmats-turbo
  ☆260Updated 6 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆507Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆465Updated 2 weeks ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆390Updated last week
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆510Updated 3 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆504Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆439Updated 2 weeks ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆308Updated 4 years ago