etkayapar/bamRefine

Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog

Language: Python - Size: 4.72 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

iliapopov17/The-shadow-of-HIV

Repository for course project in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 30 MB - Last synced: 37 minutes ago - Pushed: 1 day ago - Stars: 0 - Forks: 1

mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

Language: Python - Size: 11.7 MB - Last synced: 1 day ago - Pushed: 16 days ago - Stars: 441 - Forks: 73

nf-core/hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Language: Nextflow - Size: 5.11 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 18 - Forks: 4

ngless-toolkit/ngless

NGLess: NGS with less work

Language: Haskell - Size: 14.2 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 143 - Forks: 25

seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Language: C++ - Size: 20.7 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 389 - Forks: 80

wheretrue/biobear

Work with bioinformatic files using Arrow, Polars, and/or DuckDB

Language: Rust - Size: 1020 KB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 122 - Forks: 7

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: 2 days ago - Pushed: 20 days ago - Stars: 149 - Forks: 10

jlanga/smsk_popoolation

Snakemake pipeline for Popoolation and Popoolation2

Language: Perl - Size: 16.1 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 5 - Forks: 2

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

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

biowasm/biowasm

WebAssembly modules for genomics

Language: C - Size: 5.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 183 - Forks: 18

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

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

qPCR4vir/seqan3 Fork of seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Language: C++ - Size: 13 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

lvn3668/samtoolsparsers

Parses Samtools output and extracts flagstat results such as number of reads that are pass/fail that are properly aligned, etc.

Language: Python - Size: 2.15 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

lvn3668/pileupnotationvariantcaller

Variant caller from pileup notation / samtools alignment

Language: Python - Size: 117 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

rpianezza/GenomeDelta

Library-free horizontal transfer detection, with a focus on transposable element invasions

Language: Shell - Size: 54.5 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 0

Robaina/filterSAM

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

Language: Python - Size: 313 KB - Last synced: 16 days ago - Pushed: 11 months ago - Stars: 3 - Forks: 0

Nucleomics-VIB/admin-tools

sysadmin tasks made easier

Language: Shell - Size: 253 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

PulmonomicsLab/mcdr-mtb-standalone

Multi-class classification of drug resistance in MTB clinical isolates

Language: Shell - Size: 5.56 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

BBCG/epialleleR

Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package

Language: R - Size: 72.6 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 3 - Forks: 1

asw0049/phdscripts

This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.

Language: Shell - Size: 13.7 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

digo4/Clinical-Genomics

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

Language: Shell - Size: 190 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

SanojPunchihewa/f5n

Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com

Language: Java - Size: 123 MB - Last synced: 27 days ago - Pushed: almost 3 years ago - Stars: 10 - Forks: 7

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

qingxiangguo/Tools-for-Cancer-Genome-Analysis

Installation and usage for various tools for cancer genomics

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

LBGC-CFB/SpliceLauncher

RNAseq pipeline for alternative splicing junctions

Language: R - Size: 35 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 8

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

anita-brzoza/university_projects

The repository contain directories of projects done during the bioinformatics degree program

Language: HTML - Size: 894 KB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

ionCRAM/ionCRAM

https://ioncram.saudigenomeproject.com/

Language: C - Size: 24.1 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 1

wennj/pileupReformater

Convert output from Samtools pileup into a matrix.

Language: Java - Size: 25.4 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

nyuhuyang/RNAseq_pipeline

Pipeline of somatic variant analysis using Waldenstrom macroglobulinemia patient’s RNA-seq data, including tools like STAR, HTseq, VarScan in parallel computing in SGE clusters, Deseq2 and GSEA in R

Language: HTML - Size: 3.71 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

jlanga/smsk_tuxedo2

snakemake files of the tuxedo v2 pipeline from Pertea et al 2016

Language: Python - Size: 8.88 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 1 - Forks: 2

chgibb/unMappedCIGARFragments

Extract unmapped read fragments from a sequence alignment map by evaluating it's concise idiosyncratic gapped alignment reports (CIGARs)

Language: TypeScript - Size: 577 KB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

LidiaGS/g-d_algorithm

Language: Python - Size: 47.9 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 1

MatveySprindzuk/GenomicsSoftware

software for processing tuberculosis whole genome data. interface to the BWA, VarScan, SamTools etc.

Size: 2.85 MB - Last synced: 7 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

IARCbioinfo/needlestack

Multi-sample somatic variant caller

Language: R - Size: 49.8 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 46 - Forks: 14

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

TC-Hewitt/MuTrigo

pipeline for mutant gene candidate discovery

Language: Python - Size: 81.1 KB - Last synced: 8 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

lipingfangs/Panlineal

Panlineal is capable of generating Vgs from multiple genome alignments in form of lineal pan-genome. Combining short reads data, it can also detect the the allelism conduced by PAVs combinations of vast samples in a species.

Language: Python - Size: 10.6 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

wwick/coverageCalc

depiction of read distribution for outlier genes

Language: HTML - Size: 16.4 MB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

erinyoung/ACI

Some NGS library preps use amplicons, and it can be difficult to determine the coverage and depth of each amplicon.

Language: Python - Size: 4.64 MB - Last synced: 24 days ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

vidboda/BamCramConvert

script to convert bam2cram and reverse using find and samtools

Language: Shell - Size: 43.9 KB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

alexpreynolds/tabix-service

A nodejs-based service for requests for tabix-indexed genomic data

Language: JavaScript - Size: 124 KB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 4

kazar4/Bam-Downsampler

Script to preform downsampling on a BAM file

Language: Python - Size: 2.97 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

cyverseuk/samtools

Language: Shell - Size: 10.7 KB - Last synced: 9 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

cyverseuk/Tophat2

Language: Shell - Size: 25.4 KB - Last synced: 9 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

tiagofilipe12/pATLASflow

A pipeline to run mapping, mash screen and assembly methods for pATLAS.

Language: Python - Size: 87.9 KB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 2

mcjmigdal/sumsamstats

summarising outputs of samtools stats with ATAC-seq qc in mind

Language: R - Size: 200 KB - Last synced: 10 months ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0

afreeorange/autozygosity

A public, web-based homozygosity mapping tool

Language: Python - Size: 3.51 MB - Last synced: 12 days ago - Pushed: almost 10 years ago - Stars: 1 - Forks: 1

teepean/BAM-Analysis-Kit

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

victoria-r/TranscriptomeAssembly

Basic transcriptome assembly using Trinity and TrinityDeNovo.

Language: Shell - Size: 1.95 KB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

y9c/cpup

Convert mpileup format to base count tsv table

Language: C++ - Size: 652 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

odb9402/CNNPeaks

The ChIP-Seq peak calling algorithm using convolution neural networks

Language: Python - Size: 16.2 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 13 - Forks: 3

Sydney-Informatics-Hub/IndexReferenceFasta-nf

Create required reference genome index files for WGS data analysis

Language: Nextflow - Size: 71.3 KB - Last synced: 26 days ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

furkanmtorun/rna-seq-workflow 📦

🛠 under active development | RNA-Seq Workflow in Jupyter Notebook

Language: Jupyter Notebook - Size: 30.3 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 3 - Forks: 1

kpatel427/bash

useful bash one-liners and scripts

Language: Shell - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

cfarkas/variants2genes

Obtaining case-associated variants and correspondent genes (from control/case experiments) in BASH/R enviroment

Language: R - Size: 285 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

mnievesc/Ancient_mtDNA_Pipeline

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

Language: Shell - Size: 155 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 7 - Forks: 3

CNuge/snp-placer

Take information about snps on short sequence reads and accurately place the snps in a reference genome

Language: Python - Size: 136 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

fachrulm/GenomeComparer

For comparing the subgenomes of wheat

Language: Python - Size: 26.4 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 3 - Forks: 0

RhettRautsaw/VariantCaller

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

Language: Python - Size: 22.5 KB - Last synced: 12 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

nylander/FastEAR

FastEAR - Fast(er) Extraction of Alignment Regions from FASTA

Language: Shell - Size: 31.3 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 2

hisplan/docker-samtools

Dockerized samtools

Language: Dockerfile - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

yangao07/fxtools

fxtools: light-weight processing tool for FASTA/FASTQ/BAM format data

Language: C - Size: 5.4 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

FaithGriffin/CandidaPhylo

Focused on constructing a phylogenetic tree from Philippine strains of Candida albicans.

Language: wdl - Size: 102 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

irods-contrib/metalnx-msi

Metalnx Micro Services for iRODS

Language: C++ - Size: 12.9 MB - Last synced: about 2 months ago - Pushed: about 6 years ago - Stars: 4 - Forks: 4

brainstorm/bwa-nextflow-benchmark

Small test to compare AWS and HPC on a very simple workflow

Language: Shell - Size: 713 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 3 - Forks: 0

AmirHoseinSafari/Genotype-collector-and-SNP-dataset-creator

Collecting Genotypes from ENA and make their SNPs

Language: Python - Size: 40 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 5 - Forks: 0

hiruna72/f5n Fork of SanojPunchihewa/f5n

Genopo a.k.a. F5N - a portable DNA analysis toolkit for nanopore data https://nanoporetech.com

Language: Java - Size: 39 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

AntoineHo/HilMa

Hilbert Mapper is a C++ implementation of Hilbert's space filling curve to represent read coverage on genomic sequences. Although it can be used to represent any unidimensional vector of positive numerical data.

Language: C++ - Size: 139 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

Grelot/reserveBenefit--snpsdata_analysis

Codes i wrote for the paper "genomic resources for Mediterranean fishes"

Language: Shell - Size: 2.85 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

celalp/parse_pileup

Parse pileup files, generate consensus fasta and calculate heteroplasmy per nucleotide

Language: Python - Size: 27.3 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

r3fang/CRESTseq

CREST-seq peak calling.

Language: C++ - Size: 2.21 MB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 3 - Forks: 0

oicr-gsi/bam-qc-metrics

Metrics for BAM file QC

Language: Python - Size: 10.1 MB - Last synced: 27 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

guigolab/sambamBench-nf

A simple Nextflow pipeline for testing the performance of sambamba vs samtools

Language: Nextflow - Size: 813 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 3 - Forks: 3

hiruna72/samtools Fork of samtools/samtools

[CMake build] Tools (written in C using htslib) for manipulating next-generation sequencing data

Language: C - Size: 15 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

Grelot/diabetesGenetics--COAT

COverage Analysis Tool have been developed in 2016. It aims to automatically find bad quality regions of coding sequences in a set of sequencing data. It includes a graphical interface.

Language: Python - Size: 171 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

innovate-invent/bampy

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

Language: Python - Size: 155 KB - Last synced: 8 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

tiagofilipe12/PlasmidCoverage Fork of jacarrico/PlasmidCoverage

Script to obtain plasmid id from WGS data using bowtie2 to map

Language: Python - Size: 189 KB - Last synced: 29 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

metamaden/seq_answers

Sequencing data preprocessing

Language: R - Size: 1.44 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

IARCbioinfo/addreplacerg-nf

Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file

Size: 19.5 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 2 - Forks: 0

rhodesch/chip-seq

workflow for bulk chip-seq

Language: Shell - Size: 261 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

tt6746690/htsget

A server implementation of htsget protocol

Language: C++ - Size: 97.7 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

hisplan/singularity-samtools

Singularity for samtools

Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0