Alternatives and similar repositories for sickle

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

• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆150Updated 10 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆254Updated 6 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆217Updated 2 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆244Updated 4 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆143Updated 5 months ago
• agordon / fastx_toolkit
  FASTA/FASTQ pre-processing programs
  ☆195Updated 3 years ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆216Updated 2 years ago
• aquaskyline / SOAPdenovo2
  Next generation sequencing reads de novo assembler.
  ☆239Updated 4 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆285Updated 11 months ago
• fbreitwieser / krakenuniq
  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
  ☆243Updated 2 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆229Updated 6 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆301Updated 3 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆282Updated 5 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆288Updated last month
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆218Updated 2 months 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…
  ☆306Updated last year
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆284Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆322Updated 3 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆250Updated last year
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆337Updated 9 months ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆269Updated 7 months ago
• ENCODE-DCC / kentUtils
  UCSC command line bioinformatic utilities
  ☆188Updated 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
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆312Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆374Updated 3 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆276Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆212Updated 3 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆279Updated 2 years ago