Alternatives and similar repositories for BAM-tricks:

Users that are interested in BAM-tricks are comparing it to the libraries listed below

• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 9 months ago
• parklab / ShatterSeek
  ☆67Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆54Updated 2 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated last month
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆62Updated this week
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆65Updated 3 weeks ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆45Updated 2 years ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 5 months ago
• parklab / bamsnap
  ☆119Updated 4 months ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆89Updated 3 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 4 months ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆59Updated 5 months ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆147Updated last month
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 4 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 7 months ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆38Updated last month
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆25Updated last month
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 6 months ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆60Updated 3 years ago
• parklab / xTea
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
  ☆107Updated last month
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆48Updated 4 years ago
• zhou-lab / biscuit
  BISulfite-seq CUI Toolkit
  ☆65Updated 2 months ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆96Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆73Updated 2 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆80Updated last month
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆95Updated 11 months ago