Alternatives and similar repositories for sam2pairwise:

Users that are interested in sam2pairwise are comparing it to the libraries listed below

• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆48Updated 4 years ago
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated 9 months ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆65Updated this week
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 4 months ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆58Updated 4 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆84Updated 6 years ago
• harvardinformatics / NGmerge
  Merging paired-end reads and removing adapters
  ☆30Updated 4 years ago
• jsh58 / NGmerge
  Merging paired-end reads and removing adapters
  ☆44Updated 4 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 4 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆94Updated 11 months ago
• ISUgenomics / SequelTools
  new repo
  ☆28Updated 3 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆58Updated 11 months ago
• TrinityCTAT / CTAT-LR-fusion
  fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector
  ☆17Updated this week
• ksahlin / isONcorrect
  Error correction of ONT transcript reads
  ☆59Updated last year
• ridgelab / JustOrthologs
  ☆35Updated 2 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 2 weeks ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆45Updated 2 years ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆88Updated 3 years ago
• chizksh / digenome-toolkit2
  Digenome-toolkit ver2.
  ☆16Updated 3 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 9 months ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆56Updated 2 months ago
• mritchielab / long_read_tools
  A catalogue of available long read sequencing data analysis tools
  ☆75Updated last month
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆59Updated this week
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 5 years ago
• CshlSiepelLab / phast
  PHAST
  ☆72Updated this week
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆28Updated 4 years ago
• nunofonseca / fastq_utils
  Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
  ☆34Updated 7 months ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆111Updated 2 months ago
• epi2me-labs / modbam2bed
  ☆47Updated 6 months ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆35Updated last year