samtools

There are 2 repositories under samtools topic.

mdshw5 / pyfaidx
Efficient pythonic random access to fasta subsequences
python bioinformatics fasta indexing dna protein genomics bgzf samtools
Language:Python 479
seqan3
seqan / seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
bioinformatics blast cpp-concepts cpp20 fasta fastq fm-index modern samtools seqan sequence-alignment sequence-analysis
Language:C++ 437
biowasm / biowasm
WebAssembly modules for genomics
awk bedtools bioinformatics bowtie2 genomics grep javascript jq minimap2 samtools sed seqtk webassembly
Language:HTML 255
wheretrue / biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
bioinformatics biology rust-bio samtools arrow python biopython duckdb polars pyarrow
Language:Rust 190
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
genomics compression fastq vcf bam sam fasta gvf 23andme gzip bgzip samtools bwa cram
Language:C 171
ngless-toolkit / ngless
NGLess: NGS with less work
haskell bioinformatics bioinformatics-pipeline samtools bwa next-generation-sequencing fastq-format fastq science ngs metagenomics genomics haskell-language
Language:Haskell 150
davetang / learning_bam_file
Learning the Sequence Alignment/Map format
samtools sam bam bam-files bam-flags
Language:Perl 113
IARCbioinfo / needlestack
Multi-sample somatic variant caller
bam-files docker negative-binomial-regression nextflow ngs pipeline regression samtools somatic-mutations variants
Language:R 52
digo4 / Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
bcftools bowtie2 bwa-mem cutadapt fastp fastqc freebayes gatk-bestpractices gatk-cnv gatk-joint-variant-calling-workflow gatk4 gatk4-haplotypecaller picard samtools trimgalore trimmomatic varscan
Language:Shell 43
nf-core / hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
nextflow nf-core pipeline workflow horizontal-gene-transfer ngs taxonomies bwa-mem bwa-mem2 fastqc genomics-visualization ggbio kraken2 krona multiqc samtools tidyverse
Language:Nextflow 26
teepean / BAM-Analysis-Kit
genome autosomal dna dna-sequences genotyping genotype samtools bam
Language:Forth 19
rpianezza / GenomeDelta
Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads
bedtools bwa-mem consensus-sequences fasta fastq genome genome-analysis genome-assembly multiple-sequence-alignment samtools transposable-element transposons
Language:Shell 17
odb9402 / CNNPeaks
The ChIP-Seq peak calling algorithm using convolution neural networks
cnn-model nvidia-docker tensorflow bioinformatics chip-seq peak-calling convolutional-neural-network gpu docker-image progressbar2 samtools ngs-analysis atac-seq
Language:Python 15
LBGC-CFB / SpliceLauncher
RNAseq pipeline for alternative splicing junctions
samtools star bedtools genome-fasta gff alternative-junctions rnaseq
Language:R 13
jslfree080 / bamscope
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)
bam-files genomics-visualization vcf samtools bam bioinformatics genomics
Language:Java 10
mnievesc / Ancient_mtDNA_Pipeline
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
ancient-dna-sequences fastq-files samtools bam-files pipeline mtdna bcftools bwa fastqc
Language:Shell 10
SanojPunchihewa / f5n
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
mobile-genomics portable-genomics sequence-alignment bioinformatics-pipeline minimap2 samtools nanopolish toolkit android
Language:Java 10
qingxiangguo / Tools-for-Cancer-Genome-Analysis
Installation and usage for various tools for cancer genomics
alignment arriba bioinformatics bwa-mem cancer conda fasterq-dump mamba picard sam samtools star tricks
Language:Python 9
adrianodemarino / Determine_sex_from_bam
Get sex info from BAM file
bam determine pandas python sam samtools sex
Language:Python 7
jlanga / smsk_popoolation
Snakemake pipeline for Popoolation and Popoolation2
ngs population genomics popoolation popoolation2 bowtie2 samtools snakemake snakemake-workflows workflow
Language:Perl 7
AmirHoseinSafari / Genotype-collector-and-SNP-dataset-creator
Collecting Genotypes from ENA and make their SNPs
snp gatk samtools ena genotype tuberculosis bwa-mem fastq-files isolate snp-calling
Language:Python 6
epialleleR
BBCG / epialleleR
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
bioconductor dna-methylation next-generation-sequencing samtools epiallele
Language:R 6
filterSAM
Robaina / filterSAM
Tools to filter SAM/BAM files by percent identity and percent of matched sequence
bioinformatics genomics samtools alignment python sequence-alignment computational-biology
Language:Python 6
yangao07 / fxtools
fxtools: light-weight processing tool for FASTA/FASTQ/BAM format data
bam-files c fasta-sequences fastq-format samtools
Language:C 5
cbp44 / samflags
Command line utility written in NodeJS to decode SAM flags to explain what they mean.
bam bioinformatics bioinformatics-scripts sam sam-bam sam-flags samtools
Language:JavaScript 4
CNuge / snp-placer
Take information about snps on short sequence reads and accurately place the snps in a reference genome
bioinformatics samtools snps align-dna-sequences genome contigs pandas variant-calling
Language:Python 4
fachrulm / GenomeComparer
For comparing the subgenomes of wheat
snakemake python wheat samtools mikado pandas gmap cufflinks
Language:Python 4
gauravrmore007 / rnaseq_pipeline
An end-to-end RNA-seq pipeline for gene expression analysis and differential expression using FASTQ data, Bowtie2, SAMtools, and R (DESeq2, Gviz, etc.).
alignment bash bioconductor bioinformatics bowtie2 data-analysis deseq2 fastq gene-expression genomics rna-seq-pipeline rsamtools rstats samtools transcriptomics gviz
Language:R 4
iliapopov17 / The-shadow-of-HIV
🦠Research project in Bioinformatics Institute 2023-2024
snakemake alpha-diversity beta-diversity differential-abundance-analysis dna hiv relative-abundances bowtie2 kraken2 maaslin2 samtools iontorrent
Language:Jupyter Notebook 4
Nucleomics-VIB / admin-tools
sysadmin tasks made easier
filesender-cmd gatk picard samtools
Language:Shell 4
y9c / cpup
Convert mpileup format to base count tsv table
bioinformatics mutations mpileup samtools rna-modifications snp-genotyping dna-modifications
Language:C++ 4
erinyoung / ACI
Some NGS library preps use amplicons, and it can be difficult to determine the coverage and depth of each amplicon.
amplicons bioinformatics coverage depth python3 samtools
Language:Python 3
etkayapar / bamRefine
Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog
ancient-dna samtools pysam population-genomics python-3
Language:Python 3
ionCRAM / ionCRAM
https://ioncram.saudigenomeproject.com/
bioinformatics compression sam samtools bam-files
Language:C 3
kpatel427 / bash
useful bash one-liners and scripts
samtools ngs multithreading ngstools exome-sequencing-analysis
Language:Shell 3
RhettRautsaw / VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
bcftools gatk gatk-bestpractices indels phasing samtools snps variant-calling
Language:Python 3