assemblerflow / flowcraft

Related projects ⓘ

Alternatives and complementary repositories for flowcraft

• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆525Updated 3 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆341Updated 2 years ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆366Updated 11 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆179Updated this week
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆300Updated 9 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆307Updated 5 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆305Updated 2 years ago
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆151Updated this week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆267Updated 3 weeks ago
• pcingola / SnpEff
  ☆252Updated last week
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆140Updated this week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆192Updated last week
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆207Updated 4 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆217Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆257Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆242Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆273Updated last month
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆204Updated 4 months ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆272Updated 2 weeks ago
• DRL / blobtools
  Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
  ☆191Updated 2 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆261Updated 4 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆255Updated 10 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆200Updated 10 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆201Updated 6 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆125Updated 2 years ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆244Updated last month
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆153Updated last year
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆299Updated 5 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆210Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆106Updated last year