bam-files

There are 1 repository under bam-files topic.

kcleal / gw
Genome browser and variant annotation
annotation-tool bam-files cram-files genome-browser vcf
Language:C++ 241
ding-lab / msisensor
microsatellite instability detection using tumor only or paired tumor-normal data
msi cancer-genomics msi-score bam-files
Language:C++ 124
davetang / learning_bam_file
Learning the Sequence Alignment/Map format
samtools sam bam bam-files bam-flags
Language:Perl 111
nsalomonis / altanalyze
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
rna-seq-data alternative-splicing scrna-seq-data bioinformatics-pipeline clustering pathway-analysis network-analysis splicing-quantification splicing-visualization python fastq-anaysis bam-files single-cell-splicing cell-cycle cell-type-classification marker-gene-analysis graphical-interface command-line-tool pagerank louvain-community-detection
Language:Python 94
slowkow / pytabix
:card_index: Retrieve data in genomic intervals with a Python interface for tabix.
bioinformatics bam-files
Language:C 83
BioJulia / BioAlignments.jl
Sequence alignment tools
bam-files sam-files sequence-alignment sequence-analysis dna-sequences biology bioinformatics smith-waterman-alignment high-throughput-sequencing biojulia
Language:Julia 60
IARCbioinfo / needlestack
Multi-sample somatic variant caller
nextflow pipeline regression bam-files variants ngs somatic-mutations negative-binomial-regression samtools docker
Language:R 48
telatin / covtobed
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
bioinformatics bioinformatics-tool bioconda bed alignments bam-files sequence-coverage
Language:C++ 44
pbenner / gonetics
Go / Golang Bioinformatics Library
bigwig genomic-ranges gtf bam-files bigwig-files coverage bioinformatics bioinformatics-containers chip-seq golang golang-library
Language:Go 40
slowkow / picardmetrics
:vertical_traffic_light: Run Picard on BAM files and collate 90 metrics into one file.
picard bam-files bioinformatics quality-control rna-seq
Language:Shell 39
EI-CoreBioinformatics / portcullis
Splice junction analysis and filtering from BAM files
portcullis junction splice-junctions bam-files filter
Language:C++ 36
BioJulia / XAM.jl
Parse and process SAM and BAM formatted files
bioinformatics sam-format bam-format sam bam sam-files bam-files biojulia
Language:Julia 27
zhpn1024 / ribotish
Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
bioinformatics ribosome-profiling orfs translation-initiation-site riboseq bam-files
Language:Python 24
jonas-fuchs / BAMdash
create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
bam-files bed-files coverage-report dashboard genbank-files interactive plotly vcf-files
Language:Python 22
PoisonAlien / somaticfreq
knowledge-based genotyping of cancer hotspots from the tumor BAM files
bam-files cancer-genomics somatic-mutations html-report
Language:C 19
USDA-VS / vSNP
vSNP -- validate SNPs
snp pipeline genomics tuberculosis brucella analysis-pipeline mycobacterium-tuberculosis-complex snps whole-genome-sequencing high high-throughput-sequencing bam-files vcf phylogenetics freebayes wgs
Language:Python 19
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
Language:TypeScript 17
luntergroup / bamsplit
Split a BAM file by haplotype support
bam-files bioinformatics haplotypes variants
Language:Python 16
ANGSD-wrapper / angsd-wrapper
Utilities for analyzing next generation sequencing data.
software ngs-analysis ngs visualization gui r bash shell wrapper population-genetics next-generation-sequencing sfs bam-files fasta genotype-likelihoods thetas inbreeding-coefficient admixture user-friendly
Language:Shell 14
BioJulia / ReadDatastores.jl
Datastores for reads, not your papa's FASTQ files.
biojulia sequencing files storage format bioinformatics bioinformatics-data biology genomics genomics-data fastq fastq-files fastq-format sam-bam sam-file sam-files bam-files bam-format
Language:Julia 11
biodata-fun / htslib_howto
Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point for more complex scripts
htslib c sam vcf-files cram-files sam-files bam-files genomic-data-analysis fastq-files
Language:C 10
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
wtsi-npg / bambi
Process Illumina instrument data into SAM/BAM/CRAM files.
bioinformatics illumina bam-files htslib
Language:C 9
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 8
DKFZ-ODCF / AlignmentAndQCWorkflows
The DKFZ alignment workflow plugin originally developed at the eilslabs
workflow bwa wgbs quality-control alignment fastq-files roddy wes bwa-mem bam-files conda-environment
Language:Python 7
harper357 / bam_spot_check
A Python3 script to quickly spot check 10 random sequences from a BAM/FASTx file.
bam-files bioinformatics blast blast-url-api fasta fastq ncbi-blast sequencing
Language:Python 7
mpieva / biohazard-tools
Udo Stenzel's biohazard-tools — a collection of command-line utilities for bioinformatics [MIRROR]
haskell bioinformatics command-line cabal bam-files
Language:Haskell 7
wckdouglas / sequencing_tools
A python package storing different tools for different NGS operations
rna-seq-analysis rna ngs ngs-analysis fastq bam-files
Language:HTML 7
Arkanosis / bamrescue
Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
bam bam-files corruption repair rescue bioinformatics
Language:Rust 6
swyder / Genomic_Utilities
next-generation-sequencing bam-files sam
5
DoubleHelixApp / DoubleHelix
Genomic data manipulation tool
bioinformatics genome genome-analysis genomics microarray wgs bam-files cram-files genetics sam-files whole-genome-sequencing
Language:Python 4
USDA-VS / vSNP3
vSNP -- validate SNPs
bam-files snps analysis-pipeline brucella freebayes genomics high-throughput-sequencing influenza mycobacterium-tuberculosis-complex phylogenetics pipeline sars-cov-2 tuberculosis vcf-files wgs whole-genome-sequencing mycobacterium-bovis mycobacterium-bovis-af2122 bwa-mem
Language:Python 4
DKFZ-ODCF / nf-bam2fastq
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
bam-files conda conversion docker fastq fastq-files nextflow singularity sorting workflow
Language:Shell 3
IARCbioinfo / addreplacerg-nf
Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file
nextflow bam-files samtools
3
ionCRAM / ionCRAM
https://ioncram.saudigenomeproject.com/
bioinformatics compression sam samtools bam-files
Language:C 3
pcantalupo / bam2circos
Visualize your BAM alignments with Circos
bam bam-files circos visualization
Language:Perl 3