Alternatives and similar repositories for trimmomatic

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

• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆235Updated 4 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆215Updated this week
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆269Updated 5 months ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆213Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆265Updated 2 weeks ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆141Updated 3 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆311Updated 3 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆292Updated 9 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆213Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆160Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆234Updated 2 months ago
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆221Updated 8 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆230Updated this week
• usadellab / Trimmomatic
  ☆256Updated last year
• aquaskyline / SOAPdenovo2
  Next generation sequencing reads de novo assembler.
  ☆234Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆231Updated this week
• jtlovell / GENESPACE
  ☆212Updated 5 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆270Updated 6 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆203Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆201Updated 4 months ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆259Updated 6 months ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆217Updated 2 years ago
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆225Updated 3 weeks ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆227Updated 6 months ago
• pcingola / SnpEff
  ☆279Updated 5 months ago
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆138Updated this week
• wwood / kingfisher-download
  Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
  ☆273Updated last month
• hillerlab / TOGA
  TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…
  ☆185Updated 3 weeks ago