samtools/htslib

C library for high-throughput sequencing data formats

Language: C - Size: 12.4 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 775 - Forks: 446

ashishtele/66DaysofData

#66DaysOfData

Language: Jupyter Notebook - Size: 6.69 MB - Last synced: 4 days ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0

BlockResearchGroup/compas_model

A universal model datastructure for design, analysis, fabrication, and construction

Language: Python - Size: 60.5 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 1 - Forks: 3

samtools/htsjdk

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

Language: Java - Size: 109 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 272 - Forks: 244

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: 5 days ago - Pushed: 5 days ago - Stars: 87 - Forks: 15

alignoth/alignoth

Creating alignment plots from bam files

Language: Rust - Size: 665 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 51 - Forks: 1

hsbadr/additive

Bindings for Additive TidyModels

Language: R - Size: 7.22 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 7 - Forks: 1

lpryszcz/bin

My bioinfo toolbox

Language: Python - Size: 81.8 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 47 - Forks: 31

showteeth/scfetch

Access and Format Single-cell RNA-seq Datasets from Public Resources

Language: R - Size: 4.44 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 23 - Forks: 2

biod/sambamba

Tools for working with SAM/BAM data

Language: D - Size: 3.86 MB - Last synced: 3 days ago - Pushed: 9 months ago - Stars: 554 - Forks: 103

mbhall88/rasusa

Randomly subsample sequencing reads

Language: Rust - Size: 13.3 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 186 - Forks: 16

juliawiggeshoff/singularity-recipes

Recipes for Singularity

Size: 27.3 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 0

kojix2/ruby-htslib

HTSlib bindings for Ruby

Language: Ruby - Size: 3.4 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 8 - Forks: 0

bio-cr/hts.cr

HTSlib bindings for Crystal

Language: Crystal - Size: 1.8 MB - Last synced: 6 days ago - Pushed: 10 days ago - Stars: 10 - Forks: 1

brainstorm/htsget-indexer

htsget Rust indexer (from BAM to {CSV, JSON, DB})

Language: Rust - Size: 4.56 MB - Last synced: 10 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

brentp/hts-python

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

Language: Python - Size: 606 KB - Last synced: 10 days ago - Pushed: about 7 years ago - Stars: 49 - Forks: 18

haruishi43/bam-cbam

PyTorch Code for BAM: Botteneck Attention Module and CBAM: Convolutional Block Attention Module

Language: Python - Size: 309 KB - Last synced: 11 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

chrovis/cljam

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

Language: Clojure - Size: 35.1 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 88 - Forks: 12

kacos2000/Win10

Win 10/11 related research

Language: PowerShell - Size: 37.1 MB - Last synced: 11 days ago - Pushed: 5 months ago - Stars: 166 - Forks: 31

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: 966 MB - Last synced: 3 days ago - Pushed: 21 days ago - Stars: 149 - Forks: 10

bioSyntax/bioSyntax

Syntax highlighting for computational biology

Language: Shell - Size: 2.53 MB - Last synced: 3 days ago - Pushed: about 1 year ago - Stars: 247 - Forks: 30

Dash/Ox.BizTalk.BAM.Framework

Lightweight framework to simplify the implementation of BAM activities.

Language: C# - Size: 36.1 KB - Last synced: 12 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

tjparnell/biotoolbox

Tools for querying and analysis of genomic data

Language: Perl - Size: 7.34 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 27 - Forks: 16

ronin-gw/PyMaSC

Python implementation to calc mappability-sensitive cross-correlation for fragment length estimation and quality control for ChIP-Seq.

Language: Python - Size: 1.9 MB - Last synced: 22 days ago - Pushed: over 3 years ago - Stars: 2 - 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: 21 days ago - Pushed: over 1 year ago - Stars: 8 - Forks: 0

Sydney-Informatics-Hub/Germline-StructuralV-nf

Germline structural variant calling pipeline for short read WGS datasets

Language: Nextflow - Size: 1.18 MB - Last synced: 26 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 3

Sydney-Informatics-Hub/bamQC-nf

Report summary statistics relating to quality of bam files with Nextflow

Language: Nextflow - Size: 1.03 MB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

amarjin6/perfumes

Perfumes web page 🧴

Language: HTML - Size: 1.07 MB - Last synced: 27 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

brentp/hts-nim-tools

useful command-line tools written to showcase hts-nim

Language: Nim - Size: 11.7 KB - Last synced: 10 days ago - Pushed: over 3 years ago - Stars: 48 - Forks: 6

jslfree080/bamscope

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

Language: Java - Size: 207 MB - Last synced: 26 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 0

danielecook/seq-collection

Language: Nim - Size: 6.83 MB - Last synced: 11 days ago - Pushed: over 3 years ago - Stars: 13 - Forks: 4

Assylzhan-Izbassar/sanaro-front

sanaro.co project frontend in Angular

Language: TypeScript - Size: 21.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

dashbuilder/dashbuilder

Dashboard composition tooling based on the Uberfire framework

Language: Java - Size: 9.97 MB - Last synced: 25 days ago - Pushed: about 1 year ago - Stars: 190 - Forks: 122

biosails/pheniqs

Fast and accurate sequence demultiplexing

Language: C++ - Size: 72.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 23 - Forks: 4

mpieva/perl-ngs

Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]

Language: Perl - Size: 16.6 KB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

biod/BioD 📦

A D library for computational biology and bioinformatics

Language: D - Size: 2.63 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 46 - Forks: 19

BioJulia/XAM.jl

Parse and process SAM and BAM formatted files

Language: Julia - Size: 2.58 MB - Last synced: 28 days ago - Pushed: about 2 months ago - Stars: 27 - Forks: 13

davetang/learning_bam_file

Learning the Sequence Alignment/Map format

Language: Perl - Size: 116 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 106 - Forks: 21

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: about 1 month ago - Pushed: over 3 years ago - Stars: 855 - Forks: 123

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: 75.4 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 12 - Forks: 7

sbslee/fuc

Frequently used commands in bioinformatics

Language: Python - Size: 1.17 MB - Last synced: 9 days ago - Pushed: 8 months ago - Stars: 44 - Forks: 5

orangeSi/bam2msa

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

Language: Crystal - Size: 9.98 MB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 7 - Forks: 0

pweidner/BamQC-pipeline

Snakemake workflow to generate BAM alignment statistics on the BIH cluster.

Language: Python - Size: 68.4 KB - Last synced: 18 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

JetBrains-Research/bioinf-commons

Bioinformatics library in Kotlin

Language: Kotlin - Size: 2.4 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 31 - Forks: 3

brentp/bedder-rs

an API for intersections of genomic data

Language: Rust - Size: 174 KB - Last synced: 11 days ago - Pushed: 10 months ago - Stars: 4 - Forks: 0

chgibb/PHAT

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

Language: TypeScript - Size: 649 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 17 - Forks: 2

grailbio/gql

Query language for bioinformatic data

Language: Go - Size: 298 KB - Last synced: 26 days ago - Pushed: over 4 years ago - Stars: 7 - Forks: 2

Genetalks/gtz

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

Size: 1.53 GB - Last synced: 3 days ago - Pushed: about 2 years ago - Stars: 170 - Forks: 39

bamlab/dev-standards 📦

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

Language: JavaScript - Size: 3.35 MB - Last synced: 27 days ago - Pushed: over 5 years ago - Stars: 86 - Forks: 30

DanArmor/ai-algorithms

AI algorithms visualization made with Rust

Language: Rust - Size: 17.5 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

maragkakislab/samql

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

Language: Go - Size: 65.4 KB - Last synced: 3 months ago - Pushed: 8 months ago - Stars: 24 - Forks: 5

RezaDastranj/GAMM-ASDRs

Generalized Additive Forecasting Mortality

Language: CSS - Size: 749 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

adrianodemarino/Determine_sex_from_bam

Get sex info from BAM file

Language: Python - Size: 38.1 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

masikol/con-hi

The program annotates low-coverage regions of sequences in fasta format

Language: Python - Size: 180 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

MahdiyarMM/Memristive-Associative-Memory

HSPICE implementation of hybrid CMOS/Memristor BAM

Language: Roff - Size: 111 KB - Last synced: 5 months ago - Pushed: over 3 years ago - Stars: 5 - Forks: 0

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: 24 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 0

Computational-Genomics-BSC/GenomeMosaicMaker

Tool for copying read-alignments regions centered around variants (in VCF/VCF.GZ/BCF format) from existing genomes (in SAM/BAM/CRAM format) to insert them into canvas genomes (in SAM/BAM/CRAM format).

Language: Python - Size: 239 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

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: 2 days ago - Pushed: about 2 years ago - Stars: 5 - Forks: 1

0-Ioniel-0/guppy_MR

Repository for scripts used to estimate guppy (Poecilia reticulata) mutation rate.

Language: Python - Size: 664 KB - Last synced: 6 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 1

lindenb/hts-rdf

Managing sequencing data with RDF

Language: Makefile - Size: 90.8 KB - Last synced: 4 months ago - Pushed: 8 months ago - Stars: 11 - Forks: 0

lzyqd98/BAM

BAM

Language: Python - Size: 4.88 KB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

PavelShep/Portfolio

This portfolio(not about me), meticulously crafted according to a design mockup using HTML, SCSS, and JavaScript

Language: HTML - Size: 1.7 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

lindenb/igvfox

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

Language: JavaScript - Size: 352 KB - Last synced: 7 months ago - Pushed: over 9 years ago - Stars: 5 - Forks: 0

edgardomortiz/sam2consensus

Get the consensus sequences from SAM (and BAM) files, ignoring the reference

Language: Python - Size: 63.5 KB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 8 - Forks: 3

tuenhidiy/DIGITAL_CLOCK_MATRIX_32x32

Language: C++ - Size: 10.7 KB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 0 - 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: 7 months ago - Pushed: almost 5 years ago - Stars: 5 - Forks: 0

ViktorKostin/delta-nucmer-converter-to-bam

Converter Nucmer delta to bam

Language: Python - Size: 8.79 KB - Last synced: 8 months ago - Pushed: almost 3 years ago - Stars: 1 - 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: 4 months ago - Pushed: almost 4 years ago - Stars: 27 - Forks: 7

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: 6 days ago - Pushed: over 6 years ago - Stars: 3 - Forks: 0

stjude/teltale

Compute telomeric read fractions in a BAM file.

Language: C++ - Size: 761 KB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

stjude/fuzzion

Fuzzy fusion finder for next generation sequencing data.

Language: C++ - Size: 9.77 KB - Last synced: 8 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 2

Kulyomin/Processing24-Landing

Landing page for work

Language: HTML - Size: 605 KB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

broadinstitute/viral-ngs

Viral genomics analysis pipelines

Language: Python - Size: 64.5 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 180 - Forks: 66

sigven/cacao

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Language: R - Size: 20.4 MB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 21 - Forks: 4

Harpeng/balaplanar

Балапланар

Language: CSS - Size: 3.9 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

Harpeng/mesto-project

Проект: Место

Language: JavaScript - Size: 20.9 MB - Last synced: 5 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

sghignone/samtools

SAMtools and BCFtools (v1.10) for manipulating next-generation sequencing data, from bioconda

Language: Dockerfile - Size: 1000 Bytes - Last synced: 9 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

sghignone/pilon

Docker based on bioconda distribution (v.1.23), with fixed memory issue

Language: Dockerfile - Size: 6.84 KB - Last synced: 9 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

y9c/mpileup

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

Language: Rust - Size: 521 KB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-minibam

Language: JavaScript - Size: 146 KB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 2

Anton-Laid/TREVER-Russian

Учебный проект "Путешествия по России"

Language: CSS - Size: 2.32 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Anton-Laid/implemented-store-projects

Реализованные проекты магазинов

Language: SCSS - Size: 12.7 MB - Last synced: 9 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

Anton-Laid/mesto-react

Сервис Mesto (версия на React) — пользователи, как в Инстаграме, добавляют фотографии, ставят лайки. Это основная проектная работа в Яндекс.Практикуме сразу по многим темам

Language: JavaScript - Size: 3.27 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

ababaian/bioSyntax-archive 📦

Syntax highlighting for computational biology

Language: Vim script - Size: 22.5 MB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 16 - Forks: 2

m-clark/gammit

Functions for using mgcv for mixed models. 📈

Language: R - Size: 5.72 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 12 - Forks: 2

PaulAsaf2/how-to-learn

How to learn

Language: HTML - Size: 1.41 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

huyz1117/BAM

Implementation of BAM: Bottleneck Attention Module with TensorFLow

Language: Python - Size: 1000 Bytes - Last synced: 18 days ago - Pushed: over 5 years ago - Stars: 11 - Forks: 2

sjaenick/bamstats

bamstats: BAM alignment statistics per reference sequence

Language: C - Size: 11.7 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

Juke34/SAPiN

Summarize Aalignment Pile by Nucleotide

Language: Python - Size: 8.38 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 0

quinlan-lab/hts-python Fork of brentp/hts-python

pythonic wrapper for htslib

Language: Python - Size: 605 KB - Last synced: 18 days ago - Pushed: almost 7 years ago - Stars: 23 - Forks: 7

sneuensc/mapache

mapping pipeline for ancient DNA

Language: Python - Size: 1.61 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 23 - Forks: 1

sivkri/bam2bai

create bai file from respective bam file

Language: Shell - Size: 0 Bytes - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

developer0hye/ZAM

ZAM: Zero parameter Attention Module

Language: Python - Size: 2.86 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 24 - Forks: 5

LieberInstitute/megadepth

R interface to megadepth: BigWig and BAM related utilities

Language: R - Size: 640 KB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 11 - Forks: 2

teepean/BAM-Analysis-Kit

Language: Forth - Size: 2.18 GB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 18 - Forks: 6

biowdl/BamMetrics

A BioWDL workflow for gathering metrics from a BAM file. Category:Single-Sample

Language: wdl - Size: 1.6 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 6

tomwhite/bamreport

Produce a report on a BAM file listing useful information

Language: Java - Size: 116 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

unkaktus/rose

Gravitational wave volume visualizations

Language: Jupyter Notebook - Size: 2.63 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 1

mbhall88/fast5seek 📦

Subset of fast5 files contained in a fastq, BAM, or SAM file.

Language: Python - Size: 4.05 MB - Last synced: 10 days ago - Pushed: about 1 year ago - Stars: 11 - Forks: 2

bio-cr/bam-filter

Use simple expressions to filter a BAM/CRAM file

Language: C - Size: 63.5 KB - Last synced: 6 days ago - Pushed: 3 months ago - Stars: 5 - Forks: 0