Alternatives and similar repositories for sickle:

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

• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆221Updated 4 years ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆286Updated 5 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆131Updated 10 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆355Updated 2 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆136Updated 3 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆300Updated last month
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆209Updated last year
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆330Updated 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 / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆208Updated 3 weeks ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆207Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆212Updated 8 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated last week
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆257Updated 2 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆237Updated last year
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆194Updated last month
• pcingola / SnpEff
  ☆265Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆250Updated last year
• tpoorten / dotPlotly
  Generate an interactive dot plot from mummer or minimap alignments
  ☆197Updated last year
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆221Updated last week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆317Updated 9 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆133Updated 2 years ago
• usadellab / Trimmomatic
  ☆239Updated 9 months ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆215Updated 2 years ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆201Updated 2 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆338Updated 2 weeks ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 5 months ago