Alternatives and similar repositories for trimmomatic

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

• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆282Updated 8 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆242Updated 4 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆276Updated last month
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆225Updated 3 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆245Updated 3 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆216Updated last year
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 3 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆298Updated 3 weeks ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆217Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆275Updated 2 years ago
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆225Updated 8 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆271Updated 2 years ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆205Updated last month
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• aquaskyline / SOAPdenovo2
  Next generation sequencing reads de novo assembler.
  ☆236Updated last month
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆237Updated this week
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆326Updated 6 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆277Updated 2 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆213Updated last week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆283Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆240Updated this week
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆109Updated 2 years ago
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆307Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• usadellab / Trimmomatic
  ☆271Updated last week
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆215Updated 2 years ago
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆181Updated last week
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆234Updated 9 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆154Updated last year