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
  ☆438Updated 3 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆455Updated last year
• usadellab / Trimmomatic
  ☆274Updated last month
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆531Updated 4 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆428Updated last year
• hbctraining / DGE_workshop
  ☆402Updated 3 years ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆505Updated this week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆762Updated last week
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆348Updated this week
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆520Updated 2 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆445Updated 11 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆557Updated last week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆300Updated 2 years ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆474Updated 3 weeks ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆261Updated 2 years ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆746Updated 4 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆677Updated 5 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆403Updated 4 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆543Updated 2 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆299Updated 2 months ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆424Updated this week
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆317Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆556Updated last year
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆390Updated 2 months ago
• marcelm / cutadapt
  Cutadapt removes adapter sequences from sequencing reads
  ☆566Updated this week
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆276Updated 2 years ago
• Xinglab / rmats-turbo
  ☆282Updated last month
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆514Updated 2 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆329Updated 4 years ago