Projects in Awesome Lists tagged with bam

https://github.com/samtools/htslib

C library for high-throughput sequencing data formats

bam bcf bioinformatics cram htslib ngs sam vcf

Last synced: 29 Dec 2025

https://github.com/biod/sambamba

Tools for working with SAM/BAM data

bam bioinformatics sam

Last synced: 18 Feb 2026

https://github.com/samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 14 May 2025

https://github.com/biosyntax/biosyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 07 Apr 2025

https://github.com/bioSyntax/bioSyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 05 May 2025

https://github.com/mbhall88/rasusa

Randomly subsample sequencing reads or alignments

alignment bam bioinformatics coverage downsample fasta fastq genome-analysis random rust subsampling

Last synced: 19 Feb 2026

https://github.com/dashbuilder/dashbuilder

Dashboard composition tooling based on the Uberfire framework

bam dashboard dashbuilder elasticsearch gwt java kpi metric monitoring

Last synced: 16 May 2025

https://github.com/broadinstitute/viral-ngs

Viral genomics analysis pipelines

bam fastq genome genome-assembly genome-sequencing genomics illumina variant-annotations variant-calling viral viral-ngs

Last synced: 03 Apr 2026

https://github.com/kacos2000/win10

Win 10/11 related research

amcache bam dfir eventlog events forensic jumplist keyword-lists keywords mediaplayer-library notifications objectid sticky-notes timeline wdi win10 win11 windows xml yourphone

Last synced: 13 Apr 2025

https://github.com/kacos2000/Win10

Win 10/11 related research

amcache bam dfir eventlog events forensic jumplist keyword-lists keywords mediaplayer-library notifications objectid sticky-notes timeline wdi win10 win11 windows xml yourphone

Last synced: 09 Apr 2025

https://github.com/divonlan/genozip

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

23andme bam bgzip bwa compression cram fasta fastq genomics gvf gzip sam samtools vcf

Last synced: 13 May 2026

https://github.com/Genetalks/gtz

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

bam compress compression compression-rate fastq fastq-compression gene genomic-data-compression gtx nanopore pacbio sam

Last synced: 07 May 2025

https://github.com/chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

2bit bam bcf bed bigwig bioinformatics clojure cram fasta fastq genomics gff sam vcf wig

Last synced: 16 May 2025

https://github.com/bamlab/dev-standards

https://bamtech.gitbooks.io/dev-standards/

bam development lean standardization

Last synced: 23 Aug 2025

https://github.com/telatin/bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊

alignment bam bed bioinformatics coverage gff ngs

Last synced: 30 Oct 2025

https://github.com/mdshw5/simplesam

Simple pure Python SAM parser and objects for working with SAM records

bam bioinformatics genomics python sam

Last synced: 13 May 2025

https://github.com/brentp/hts-nim-tools

useful command-line tools written to showcase hts-nim

bam bioinformatics genomics nim nim-lang vcf vcf-filtering

Last synced: 09 Aug 2025

https://github.com/brentp/hts-python

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

bam bioinformatics fasta genomics htslib python sam

Last synced: 21 Mar 2025

https://github.com/sbslee/fuc

Frequently used commands in bioinformatics

api bam bed bioinformatics cli cram fasta fastq gff gtf maf sam vcf visualization

Last synced: 06 Apr 2025

https://github.com/lpryszcz/bin

My bioinfo toolbox

bam bioinformatics fastq filtering ngs processing python sam

Last synced: 21 Oct 2025

https://github.com/jetbrains-research/bioinf-commons

Bioinformatics library in Kotlin

2bit bam bed bioinformatics cancellable chip-seq dataframe dataset dna-sequence fasta fastq hmm hypothesis-testing kotlin methylation mixture progress sampling

Last synced: 19 Oct 2025

https://github.com/orangeSi/GSSplayground

Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature

bam bioinformatics comparative-genomics crosslink depth genecluster genome-viewer genomes igv-like indel long-reads read-mapping snp structure-variation sv svg synteny transcriptomics vcf visualization

Last synced: 18 Nov 2025

https://github.com/bamlab/nest-rabbit-tasks

nest-rabbit-worker is a TaskQueue based upon RabbitMQ for NestJS

amqp amqp0-9-1 bam nestjs nodejs rabbitmq typescript

Last synced: 17 Aug 2025

https://github.com/biojulia/xam.jl

Parse and process SAM and BAM formatted files

bam bam-files bam-format bioinformatics biojulia sam sam-files sam-format

Last synced: 15 Apr 2025

https://github.com/biosails/pheniqs

Fast and accurate sequence demultiplexing

autocomplete bam barcode classifiers cram demultiplexing fastq multiplexing robust sam sequencing tag tagging

Last synced: 27 Dec 2025

https://github.com/maragkakislab/samql

SQL-like query language for the SAM/BAM file format

bam bioinformatics go sam sequencing sql

Last synced: 12 May 2026

https://github.com/rhpvorderman/sequali

Fast sequencing data quality metrics

bam fastq illumina nanopore qc quality-control

Last synced: 14 Jun 2025

https://github.com/chgibb/PHAT

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

alignment analysis bam bam-files bioinformatics bioinformatics-analysis bioinformatics-tool circos circos-graphs circos-plot dna electron host next-generation-sequencing ngs pathogen phat quality-control snps visualization

Last synced: 05 May 2025

https://github.com/m-clark/gammit

Functions for using mgcv for mixed models. 📈

bam gam glmer lme4 lmer mgcv mixed-models random-effects variance-components

Last synced: 30 Apr 2025

https://github.com/epigen/fetch_ngs

Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.

bam database fastq genomics next-generation-sequencing ngs repository

Last synced: 14 Sep 2025

https://github.com/lieberinstitute/megadepth

R interface to megadepth: BigWig and BAM related utilities

bam bigwig daspter megadepth recount2 recount3 rstats

Last synced: 07 May 2025

https://github.com/orangesi/bam2msa

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region

alignment bam bioinformatics crystal-lang msa pairwise-alignment

Last synced: 30 Jun 2025

https://github.com/kojix2/ruby-htslib

HTSlib bindings for Ruby

bam bcf bioinformatics genomics htslib ruby sam

Last synced: 25 Aug 2025

https://github.com/orangeSi/bam2msa

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region

alignment bam bioinformatics crystal-lang msa pairwise-alignment

Last synced: 10 Jul 2025

https://github.com/lindenb/hts-rdf

Managing sequencing data with RDF

bam bioinformatics data-management ontology rdf sparql tutorial vcf

Last synced: 13 Mar 2026

https://github.com/huyz1117/BAM

Implementation of BAM: Bottleneck Attention Module with TensorFLow

attention-mechanism bam tensorflow

Last synced: 07 May 2025

https://github.com/bio-cr/hts.cr

HTSlib bindings for Crystal

bam bcf bioinformatics crystal crystal-bindings genomics htslib

Last synced: 03 Jul 2025

https://github.com/jslfree080/bamscope

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)

bam bam-files bioinformatics genomics genomics-visualization samtools vcf

Last synced: 18 Nov 2025

https://github.com/mrfearless/infinityenginelibraries

Infinity Engine Libraries for assembler x86

asm baldurs-gate bam bif biff bioware chitin erf infinity-engine library masm rim winbif x86

Last synced: 16 Jun 2025

https://github.com/arkanosis/bamrescue

Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them

bam bam-files bioinformatics corruption repair rescue

Last synced: 13 Apr 2025

https://github.com/grailbio/gql

Query language for bioinformatic data

bam bioinformatics golang

Last synced: 23 Jun 2025

https://github.com/lpryszcz/rediscover

RNA editing discovery from NGS data.

bam discovery editing ngs regulation rna rna-seq

Last synced: 20 Aug 2025

https://github.com/hsbadr/additive

Bindings for Additive TidyModels

additive bam gam generalized-additive-models mgcv r tidymodels

Last synced: 01 Jul 2025

https://github.com/brentp/bpbio

basepair bio: a single binary with many useful genomics subtools.

bam cram genomics genomics-visualization high-throughput-sequencing structural-variation

Last synced: 28 Jun 2025

https://github.com/bio-cr/bam-filter

Use simple expressions to filter a BAM/CRAM file

bam bioinformatics crystal genomics htslib

Last synced: 20 Aug 2025

https://github.com/erwinkramer/otel-business

Get started with distributed business tracing in context of OTel (OpenTelemetry).

application-insights azure azure-application-insights azure-monitor bam business-activity-monitor open-telemetry opentelemetry otel

Last synced: 22 Aug 2025

https://github.com/lindenb/igvfox

firefox addon : IGV (Integrative Genomics Viewer) control through mozilla Firefox

addon bam bioinformatics firefox genomics igv javascript mozilla-firefox plugin socket visualization xpi

Last synced: 27 May 2026

https://github.com/sydney-informatics-hub/germline-structuralv-nf

Germline structural variant calling pipeline for short read WGS datasets

annotsv australian-biocommons bam bioinformatics dsl2 genomics germline-variant-calling manta nextflow ngs pipeline smoove structural-variants survivor tiddit workflow

Last synced: 02 Jan 2026

https://github.com/unkaktus/rose

Gravitational wave volume visualizations

aei apptainer bam einstein energry-flux gravitational-waves gravity paraview paraview-plugin sxs

Last synced: 23 Apr 2025

https://github.com/poisonalien/basecounts

A tool to extract ATGC/Indel read counts at user specific loci from BAM files

bam basecounts bioinformatics nucleotide-frequency readcounts sequencing wgs-data

Last synced: 14 Oct 2025

https://github.com/juke34/sapin

Summarize Alignment Pile by Nucleotide

alignment bam

Last synced: 02 Mar 2026

https://github.com/brentp/bedder-rs

an API for intersections of genomic data

bam bed bioinformatics cram genomics vcf

Last synced: 29 Oct 2025

https://github.com/pcantalupo/bam2circos

Visualize your BAM alignments with Circos

bam bam-files circos visualization

Last synced: 29 Jul 2025

https://github.com/msk-access/nucleo

Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK

bam msk-access umi

Last synced: 10 Feb 2026

https://github.com/mrfearless/infinityenginelibraries64

Infinity Engine Libraries for assembler x64

asm baldurs-gate bam bif biff bioware chitin erf infinity-engine library rim uasm winbif x64

Last synced: 10 Apr 2025

https://github.com/gear-genomics/halo

Halo: Haplotype processor

alignment bam haplotypes single-cell

Last synced: 17 Jan 2026

https://gitlab.com/tprodanov/pileuppy

Colorful and fast BAM pileup.

bam bioinformatics pileup

Last synced: 03 Dec 2025

https://github.com/georgiesamaha/fq2vcf

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.

bam bioinformatics gatk genomics indels mapping ngs pipeline snps variant-calling vcf

Last synced: 15 Mar 2025

https://github.com/alexpreynolds/convert2bed

Convert common binary and text genomic formats to BED

bam bed c conversion

Last synced: 16 May 2025

https://github.com/y9c/mpileup

extract nucleotide/read counts at user specific loci from multiple bam files

bam modification mutation rust snp

Last synced: 07 Jul 2025

https://github.com/innovate-invent/bampy

Python implementation of htslib supporting BAM, SAM, and BGZF compression

bai bam bgzf hts htslib sam samtools

Last synced: 18 Jan 2026

https://github.com/biowdl/bam-to-gvcf

A BioWDL workflow for generating gVCF files from BAM files.

bam haplotypecaller pipeline wdl

Last synced: 17 Mar 2026

https://github.com/fulcrumgenomics/ref-solver

Identify which human reference genome was used to align a BAM/SAM/CRAM file

bam bioinformatics cram genomics grch37 grch38 hg19 hg38 reference-genome rust sam

Last synced: 17 Mar 2026

https://github.com/lityrgia/silent-injector

Manual map injector which cleaning itself from different places after inject

bam shell-bags silent-injector

Last synced: 24 Feb 2025

https://github.com/darealfreak/teeworlds-docker-windows-build

providing a clean windows environment to compile teeworlds for windows

bam docker teeworlds

Last synced: 01 May 2026

https://github.com/giatraskon/chromosome11-variantcalling-gatk

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

1000genomes bam bcftools bioinformatics bwa exome-sequencing gatk gatk4-haplotypecaller genome-analysis haplotypecaller human-genome indels population-genetics reference-genome samtools snpeff snps variant-annotation variant-calling vcf