Topic: "bam"
samtools/htslib
C library for high-throughput sequencing data formats
Language: C - Size: 12.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 892 - Forks: 458
implus/PytorchInsight
a pytorch lib with state-of-the-art architectures, pretrained models and real-time updated results
Language: Python - Size: 5.09 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 857 - Forks: 122
biod/sambamba
Tools for working with SAM/BAM data
Language: D - Size: 3.87 MB - Last synced at: 26 days ago - Pushed at: about 1 year ago - Stars: 597 - Forks: 104
samtools/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
Language: Java - Size: 164 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 291 - Forks: 242
bioSyntax/bioSyntax
Syntax highlighting for computational biology
Language: Shell - Size: 2.53 MB - Last synced at: 8 months ago - Pushed at: almost 3 years ago - Stars: 265 - Forks: 30
mbhall88/rasusa
Randomly subsample sequencing reads or alignments
Language: Rust - Size: 13.5 MB - Last synced at: 4 days ago - Pushed at: 8 days ago - Stars: 250 - Forks: 20
broadinstitute/viral-ngs
[THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble https://github.com/broadinstitute/viral-phylo https://github.com/broadinstitute/viral-classify https://github.com/broadinstitute/viral-pipelines
Language: Python - Size: 64.5 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 195 - Forks: 67
dashbuilder/dashbuilder
Dashboard composition tooling based on the Uberfire framework
Language: Java - Size: 9.97 MB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 192 - Forks: 120
kacos2000/Win10
Win 10/11 related research
Language: PowerShell - Size: 37.1 MB - Last synced at: 9 months ago - Pushed at: about 2 years ago - Stars: 184 - Forks: 32
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
Language: C - Size: 1.06 GB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 171 - Forks: 15
Genetalks/gtz
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
Size: 1.53 GB - Last synced at: 8 months ago - Pushed at: over 3 years ago - Stars: 170 - Forks: 40
davetang/learning_bam_file
Learning the Sequence Alignment/Map format
Language: Perl - Size: 116 MB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 113 - Forks: 23
chrovis/cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
Language: Clojure - Size: 35.7 MB - Last synced at: 24 days ago - Pushed at: 25 days ago - Stars: 92 - Forks: 13
Griffan/VerifyBamID
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
Language: mupad - Size: 69.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 89 - Forks: 15
bamlab/dev-standards 📦
https://bamtech.gitbooks.io/dev-standards/
Language: JavaScript - Size: 3.35 MB - Last synced at: 5 months ago - Pushed at: about 7 years ago - Stars: 86 - Forks: 29
Mohammedcha/FaceBook-BAM-Quiz-Instant-Game
FaceBook Instant Game - BAM Quiz
Language: JavaScript - Size: 262 KB - Last synced at: almost 3 years ago - Pushed at: almost 7 years ago - Stars: 76 - Forks: 46
alignoth/alignoth
Creating alignment plots from bam files
Language: Rust - Size: 1.29 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 67 - Forks: 1
telatin/bamtocov
🏔 coverage extraction from BAM/CRAM files, supporting targets 📊
Language: Nim - Size: 33.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 65 - Forks: 7
mdshw5/simplesam
Simple pure Python SAM parser and objects for working with SAM records
Language: Python - Size: 133 KB - Last synced at: 8 months ago - Pushed at: over 3 years ago - Stars: 64 - Forks: 8
sbslee/fuc
Frequently used commands in bioinformatics
Language: Python - Size: 1.21 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 57 - Forks: 7
lpryszcz/bin 📦
My bioinfo toolbox
Language: Python - Size: 81.9 MB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 50 - Forks: 31
brentp/hts-nim-tools
useful command-line tools written to showcase hts-nim
Language: Nim - Size: 11.7 KB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 50 - Forks: 6
brentp/hts-python
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
Language: Python - Size: 606 KB - Last synced at: 4 months ago - Pushed at: almost 9 years ago - Stars: 49 - Forks: 18
biod/BioD 📦
A D library for computational biology and bioinformatics
Language: D - Size: 2.63 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 46 - Forks: 19
showteeth/GEfetch2R
GEfetch2R - Access Single-cell/Bulk RNA-seq Data from Public Repositories and Benchmark the Subsequent Format Conversion Tools
Language: R - Size: 34.7 MB - Last synced at: 20 days ago - Pushed at: 21 days ago - Stars: 39 - Forks: 4
sneuensc/mapache
mapping pipeline for ancient DNA
Language: Python - Size: 1.52 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 34 - Forks: 5
JetBrains-Research/bioinf-commons
Bioinformatics library in Kotlin
Language: Kotlin - Size: 2.38 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 34 - Forks: 3
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
Language: HTML - Size: 148 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 33 - Forks: 8
rhpvorderman/sequali
Fast sequencing data quality metrics
Language: C - Size: 9.47 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 31 - Forks: 0
bamlab/nest-rabbit-tasks
nest-rabbit-worker is a TaskQueue based upon RabbitMQ for NestJS
Language: TypeScript - Size: 1.39 MB - Last synced at: 2 months ago - Pushed at: about 3 years ago - Stars: 30 - Forks: 4
BioJulia/XAM.jl
Parse and process SAM and BAM formatted files
Language: Julia - Size: 2.65 MB - Last synced at: 4 months ago - Pushed at: 9 months ago - Stars: 29 - Forks: 14
biosails/pheniqs
Fast and accurate sequence demultiplexing
Language: C++ - Size: 72.2 MB - Last synced at: 10 days ago - Pushed at: 7 months ago - Stars: 28 - Forks: 4
maragkakislab/samql
SQL-like query language for the SAM/BAM file format
Language: Go - Size: 65.4 KB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 5
tjparnell/biotoolbox
Tools for querying and analysis of genomic data
Language: Perl - Size: 9.04 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 16
developer0hye/ZAM
ZAM: Zero parameter Attention Module
Language: Python - Size: 2.86 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 24 - Forks: 5
quinlan-lab/hts-python Fork of brentp/hts-python
pythonic wrapper for htslib
Language: Python - Size: 605 KB - Last synced at: over 1 year ago - Pushed at: over 8 years ago - Stars: 23 - Forks: 7
NTU-CCA/EE7207
EE7207 Neural & Fuzzy Systems
Language: Python - Size: 40.6 MB - Last synced at: 6 months ago - Pushed at: almost 5 years ago - Stars: 22 - Forks: 0
sigven/cacao
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Language: R - Size: 20.4 MB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 21 - Forks: 4
teepean/BAM-Analysis-Kit
Language: Forth - Size: 2.18 GB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 18 - Forks: 6
chgibb/PHAT
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Language: TypeScript - Size: 649 MB - Last synced at: 8 months ago - Pushed at: about 3 years ago - Stars: 17 - Forks: 2
ababaian/bioSyntax-archive 📦
Syntax highlighting for computational biology
Language: Vim script - Size: 22.5 MB - Last synced at: over 2 years ago - Pushed at: about 8 years ago - Stars: 16 - Forks: 2
m-clark/gammit
Functions for using mgcv for mixed models. 📈
Language: R - Size: 5.72 MB - Last synced at: 8 months ago - Pushed at: about 5 years ago - Stars: 15 - Forks: 4
BioAnalyticResource/eFP-Seq_Browser
An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.
Language: HTML - Size: 79.6 MB - Last synced at: 30 days ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 7
epigen/fetch_ngs
Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.
Language: Python - Size: 50.8 KB - Last synced at: 4 months ago - Pushed at: 7 months ago - Stars: 13 - Forks: 0
llondon6/nrutils_dev
Python API for low-level analysis of NR data: Psi4, strain, modeling, lal+pycbc interface when appropriate
Language: Jupyter Notebook - Size: 288 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 13 - Forks: 4
danielecook/seq-collection
Language: Nim - Size: 6.83 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 13 - Forks: 4
bio-cr/hts.cr
HTSlib bindings for Crystal
Language: Crystal - Size: 2.53 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 1
LieberInstitute/megadepth
R interface to megadepth: BigWig and BAM related utilities
Language: R - Size: 679 KB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 2
mbhall88/fast5seek 📦
Subset of fast5 files contained in a fastq, BAM, or SAM file.
Language: Python - Size: 4.05 MB - Last synced at: 23 days ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 2
kojix2/ruby-htslib
HTSlib bindings for Ruby
Language: Ruby - Size: 4.22 MB - Last synced at: 8 days ago - Pushed at: 21 days ago - Stars: 11 - Forks: 0
orangeSi/bam2msa
convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region
Language: Crystal - Size: 10.5 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 0
lindenb/hts-rdf
Managing sequencing data with RDF
Language: Makefile - Size: 90.8 KB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 0
huyz1117/BAM
Implementation of BAM: Bottleneck Attention Module with TensorFLow
Language: Python - Size: 1000 Bytes - Last synced at: 8 months ago - Pushed at: almost 7 years ago - Stars: 11 - Forks: 2
jslfree080/bamscope
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)
Language: Java - Size: 207 MB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 0
TRON-Bioinformatics/vafator
Annotate variants in a VCF file with technical annotations from one or more BAMs
Language: Jupyter Notebook - Size: 60.3 MB - Last synced at: 22 days ago - Pushed at: 4 months ago - Stars: 9 - Forks: 0
mrfearless/InfinityEngineLibraries
Infinity Engine Libraries for assembler x86
Language: Assembly - Size: 3.85 MB - Last synced at: 7 months ago - Pushed at: about 6 years ago - Stars: 9 - Forks: 3
hsbadr/additive
Bindings for Additive TidyModels
Language: R - Size: 8.39 MB - Last synced at: 15 days ago - Pushed at: 16 days ago - Stars: 8 - Forks: 2
Arkanosis/bamrescue
Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
Language: Rust - Size: 246 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 1
lpryszcz/REDiscover
RNA editing discovery from NGS data.
Language: Python - Size: 313 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 2
edgardomortiz/sam2consensus
Get the consensus sequences from SAM (and BAM) files, ignoring the reference
Language: Python - Size: 63.5 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 8 - Forks: 3
BlockResearchGroup/compas_model
A universal model datastructure for design, analysis, fabrication, and construction
Language: Python - Size: 36.1 MB - Last synced at: 1 day ago - Pushed at: 26 days ago - Stars: 7 - Forks: 3
PathoGenOmics-Lab/get_MNV
Identifies multiple SNVs within the same codon, reclassifies them as MNVs, and accurately computes resulting amino acid changes from genomic reads
Language: Rust - Size: 3.36 MB - Last synced at: 4 months ago - Pushed at: 11 months ago - Stars: 7 - Forks: 1
Sydney-Informatics-Hub/Germline-StructuralV-nf
Germline structural variant calling pipeline for short read WGS datasets
Language: Nextflow - Size: 1.18 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 5
MatteoSchiavinato/Utilities
General purpose tools for every-day sequencing bioinformatics. If you use any of these tools, please acknowledge this repository (there are no publications). Let's all help each other ;)
Language: Python - Size: 89.8 KB - Last synced at: almost 3 years ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 6
grailbio/gql
Query language for bioinformatic data
Language: Go - Size: 298 KB - Last synced at: 7 months ago - Pushed at: about 6 years ago - Stars: 7 - Forks: 2
nh13/rebgzf
Efficient gzip to BGZF transcoder using half-decompression (2-4x faster than decompress+recompress)
Language: Rust - Size: 147 KB - Last synced at: 16 days ago - Pushed at: 19 days ago - Stars: 6 - Forks: 0
erwinkramer/otel-business
Get started with distributed business tracing in context of OTel (OpenTelemetry).
Language: C# - Size: 5.53 MB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 6 - Forks: 0
HuntsmanCancerInstitute/UMIScripts
Simple scripts for handling Unique Molecular Indexes in Fastq and Bam files
Language: Perl - Size: 249 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0
brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
Language: Nim - Size: 96.7 KB - Last synced at: 4 months ago - Pushed at: over 6 years ago - Stars: 6 - Forks: 2
lucasrabiec/NeuralNetworks
Artificial neural networks (BCM, BAM, MLP, SOM, etc.)
Language: C# - Size: 246 KB - Last synced at: almost 3 years ago - Pushed at: almost 9 years ago - Stars: 6 - Forks: 2
lschoenm/MerKurio
Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags.
Language: Rust - Size: 4.85 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0
bio-cr/bam-filter
Use simple expressions to filter a BAM/CRAM file
Language: C - Size: 90.8 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0
brentp/bedder-rs
an API for intersections of genomic data
Language: Rust - Size: 371 KB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 0
lityrgia/selfclean-injector
Manual map injector which cleaning itself from different places after inject
Language: C++ - Size: 18.6 KB - Last synced at: 7 months ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 2
PoisonAlien/basecounts
A tool to extract ATGC/Indel read counts at user specific loci from BAM files
Language: C - Size: 38.1 KB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 1
MahdiyarMM/Memristive-Associative-Memory
HSPICE implementation of hybrid CMOS/Memristor BAM
Language: Roff - Size: 111 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 5 - Forks: 0
mnievesc/ENAH_curso_aDNA_2019
This repository contains practical data analyses exercises for the special course on Paleogenomics and Anthropology held at the National School of Anthropology of Mexico (ENAH), May 6 to 10, 2019. Topics include performing QC on aDNA NGS data, assigning mtDNA haplogroups and testing hypotheses w/PCA and ADMIXTURE analyses. No previous command-line experience needed.
Language: OpenEdge ABL - Size: 55.8 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0
lindenb/igvfox
firefox addon : IGV (Integrative Genomics Viewer) control through mozilla Firefox
Language: JavaScript - Size: 352 KB - Last synced at: about 2 years ago - Pushed at: about 11 years ago - Stars: 5 - Forks: 0
Juke34/SAPiN
Summarize Alignment Pile by Nucleotide
Language: Python - Size: 8.39 MB - Last synced at: 5 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 1
alshai/varcount
Outputs alignment coverage over a predefined set of variants
Language: C++ - Size: 59.6 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 0
ashishtele/66DaysofData
#66DaysOfData
Language: Jupyter Notebook - Size: 6.69 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 0
mgalm/bcn-scripts
BlueCat Usersscripts
Language: JavaScript - Size: 85.9 KB - Last synced at: 2 months ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 2
lindenb/x11hts
X11 related utilities for hts
Language: C++ - Size: 229 KB - Last synced at: almost 3 years ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 0
cbp44/samflags
Command line utility written in NodeJS to decode SAM flags to explain what they mean.
Language: JavaScript - Size: 7.81 KB - Last synced at: 3 months ago - Pushed at: over 8 years ago - Stars: 4 - Forks: 0
gear-genomics/halo
Halo: Haplotype processor
Language: C++ - Size: 5.78 MB - Last synced at: 9 days ago - Pushed at: 11 days ago - Stars: 3 - Forks: 1
ylab-hi/ChimeraLM
A genomic language model that detects amplification artifacts for accurate structural variant calling in long-read single-cell sequencing
Language: Python - Size: 37.8 MB - Last synced at: 2 days ago - Pushed at: 23 days ago - Stars: 3 - Forks: 0
msk-access/nucleo
Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK
Language: Common Workflow Language - Size: 951 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 3 - Forks: 1
adrianodemarino/Determine_sex_from_bam
Get sex info from BAM file
Language: Python - Size: 38.1 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0
mrfearless/InfinityEngineLibraries64
Infinity Engine Libraries for assembler x64
Language: Assembly - Size: 480 KB - Last synced at: 9 months ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 1
pcantalupo/bam2circos
Visualize your BAM alignments with Circos
Language: Perl - Size: 6.84 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 3 - Forks: 1
JMencius/BamQVFilter
Filter BAM file based on read mean QV, implemented in Rust
Language: Rust - Size: 62.5 KB - Last synced at: 16 days ago - Pushed at: 18 days ago - Stars: 2 - Forks: 0
ronin-gw/PyMaSC
Python implementation to calc mappability-sensitive cross-correlation for fragment length estimation and quality control for ChIP-Seq.
Language: Python - Size: 3.75 MB - Last synced at: 23 days ago - Pushed at: 4 months ago - Stars: 2 - Forks: 0
georgiesamaha/fq2vcf
Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.
Language: Shell - Size: 54.7 KB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1
y9c/mpileup
extract nucleotide/read counts at user specific loci from multiple bam files
Language: Rust - Size: 521 KB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0
stjude/teltale
Compute telomeric read fractions in a BAM file.
Language: C++ - Size: 761 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1
biodata-fun/nf_genomics_pipelines
This repo contains pipeline implemented using the nextflow workflow management system for the analysis of genomics data
Language: Nextflow - Size: 72.3 KB - Last synced at: almost 3 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
alexpreynolds/convert2bed
Convert common binary and text genomic formats to BED
Language: C - Size: 192 KB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 2
JerryPan2718/Microbiome-PTR
Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.
Language: C - Size: 39.1 MB - Last synced at: almost 3 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0
tprodanov/pileuppy
Colorful and fast BAM pileup.
Last synced at: about 1 month ago - Stars: 2 - Forks: 1
Computational-Genomics-BSC/GenomeVariator
Tool for adding genomic variants to an existing genome (in SAM/BAM/CRAM format). Currently supported variants are SNVs, indels and SVs (insertions, deletions, translocations, inversions and duplications). It generates realistic genomes as almost always less than 99% of the original real genome is modified.
Language: Python - Size: 15.1 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 1
