Alternatives and similar repositories for GAAS

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

• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆262Updated last month
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆215Updated 2 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆234Updated 4 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆257Updated 2 years ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆324Updated last year
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆308Updated 2 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆291Updated 8 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆206Updated 2 years ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆226Updated 5 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆138Updated 10 years ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆242Updated last year
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆139Updated 3 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆150Updated 2 years ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆212Updated last year
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆280Updated 8 months ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆203Updated 3 weeks ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆343Updated last year
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆271Updated 5 months ago
• Dfam-consortium / RepeatModeler
  De-Novo Repeat Discovery Tool
  ☆215Updated last month
• kcleal / gw
  Genome browser and variant annotation
  ☆310Updated last week
• wdecoster / chopper
  ☆198Updated 2 months ago
• jtlovell / GENESPACE
  ☆211Updated 5 months ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆387Updated last month
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆227Updated this week
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆229Updated last month
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆312Updated last year