Alternatives and similar repositories for fastx_toolkit

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

• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆239Updated last month
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆142Updated 10 years ago
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆224Updated 8 years ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆214Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆269Updated last week
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆141Updated last month
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆219Updated last month
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆275Updated 6 months ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆152Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆273Updated last year
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆202Updated 6 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆207Updated last month
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆274Updated last week
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆216Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆227Updated 2 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆236Updated last week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆296Updated this week
• aquaskyline / SOAPdenovo2
  Next generation sequencing reads de novo assembler.
  ☆236Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆157Updated 2 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆319Updated 4 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆234Updated this week
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated 3 weeks ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆153Updated 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
• fbreitwieser / krakenuniq
  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
  ☆237Updated last year
• ENCODE-DCC / kentUtils
  UCSC command line bioinformatic utilities
  ☆184Updated last year
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆305Updated last year