bam

There are 2 repositories under bam topic.

implus / PytorchInsight
a pytorch lib with state-of-the-art architectures, pretrained models and real-time updated results
pytorch classification detection state-of-the-art pretrained-models sknet senet gcnet cbam bam sge cnn cnn-tricks tricks shufflenetv2 training-shufflenetv2 convolutional-networks weight-decay attention-models weight-normalization-family
Language:Python 857
samtools / htslib
C library for high-throughput sequencing data formats
bam bcf bioinformatics cram htslib ngs sam vcf
Language:C 772
biod / sambamba
Tools for working with SAM/BAM data
bam bioinformatics sam
Language:D 553
samtools / htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
genomics sequencing dna ngs bam cram sam fasta vcf java-api java
Language:Java 271
bioSyntax / bioSyntax
Syntax highlighting for computational biology
bioinformatics computational-biology syntax-highlighting less vim gedit sublime-text bam vcf fasta pdb
Language:Shell 246
dashbuilder / dashbuilder
Dashboard composition tooling based on the Uberfire framework
bam monitoring kpi metric dashboard gwt elasticsearch java dashbuilder
Language:Java 190
broadinstitute / viral-ngs
Viral genomics analysis pipelines
viral-ngs viral genomics genome genome-assembly genome-sequencing bam fastq variant-calling variant-annotations illumina
Language:Python 186
Genetalks / gtz
A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.
compression-rate genomic-data-compression fastq-compression gtx pacbio nanopore compress compression gene fastq bam sam
170
Win10
kacos2000 / Win10
Win 10/11 related research
events notifications jumplist amcache bam dfir forensic keywords eventlog xml keyword-lists windows win10 timeline yourphone objectid wdi sticky-notes mediaplayer-library win11
Language:PowerShell 163
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 148
davetang / learning_bam_file
Learning the Sequence Alignment/Map format
samtools sam bam bam-files bam-flags
Language:Perl 109
chrovis / cljam
A DNA Sequence Alignment/Map (SAM) library for Clojure
clojure bioinformatics genomics sam bam vcf bcf fasta 2bit bed fastq wig bigwig gff
Language:Clojure 88
bamlab / dev-standards
https://bamtech.gitbooks.io/dev-standards/
development standardization lean bam
Language:JavaScript 86
Griffan / VerifyBamID
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
genetics dna-sequences qc-analysis contamination bioinformatics biostatistics bam cram
Language:mupad 84
Mohammedcha / FaceBook-BAM-Quiz-Instant-Game
FaceBook Instant Game - BAM Quiz
bam quiz instant-apps instantgames facebook
Language:JavaScript 77
mdshw5 / simplesam
Simple pure Python SAM parser and objects for working with SAM records
bam bioinformatics genomics python sam
Language:Python 61
telatin / bamtocov
🏔 coverage extraction from BAM/CRAM files, supporting targets 📊
bioinformatics bam coverage alignment gff bed ngs
Language:Nim 58
alignoth / alignoth
Creating alignment plots from bam files
alignment bam igv plots rust vega
Language:Rust 51
brentp / hts-python
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
genomics python htslib bioinformatics bam sam fasta
Language:Python 49
brentp / hts-nim-tools
useful command-line tools written to showcase hts-nim
genomics bioinformatics nim nim-lang bam vcf vcf-filtering
Language:Nim 48
lpryszcz / bin
My bioinfo toolbox
bioinformatics python ngs bam sam fastq processing filtering
Language:Python 47
biod / BioD
A D library for computational biology and bioinformatics
bioinformatics d sam bam
Language:D 46
sbslee / fuc
Frequently used commands in bioinformatics
vcf bed fastq bioinformatics api cli bam sam cram maf visualization fasta gff gtf
Language:Python 44
bamlab / nest-rabbit-tasks
nest-rabbit-worker is a TaskQueue based upon RabbitMQ for NestJS
nestjs amqp amqp0-9-1 rabbitmq nodejs typescript bam
Language:TypeScript 31
JetBrains-Research / bioinf-commons
Bioinformatics library in Kotlin
2bit bam bed bioinformatics cancellable chip-seq dataframe dataset dna-sequence fasta fastq hmm hypothesis-testing kotlin methylation mixture progress sampling
Language:Kotlin 31
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
genomes genecluster synteny crosslink bioinformatics svg vcf snp bam read-mapping depth visualization structure-variation genome-viewer sv transcriptomics igv-like comparative-genomics long-reads indel
Language:HTML 29
BioJulia / XAM.jl
Parse and process SAM and BAM formatted files
bam bam-files bam-format bioinformatics biojulia sam sam-files sam-format
Language:Julia 27
tjparnell / biotoolbox
Tools for querying and analysis of genomic data
bioinformatics bioperl bigwig bam gff3 gtf fasta chip-seq rna-seq vcf annotations
Language:Perl 27
mapache
sneuensc / mapache
mapping pipeline for ancient DNA
adna ancient-dna genomics mapping mapper pipeline workflow snakemake fastq bam
Language:Python 25
developer0hye / ZAM
ZAM: Zero parameter Attention Module
cbam bam attention attention-module zcbam self-attention zam
Language:Python 24
maragkakislab / samql
SQL-like query language for the SAM/BAM file format
bam bioinformatics go sam sequencing sql
Language:Go 24
biosails / pheniqs
Fast and accurate sequence demultiplexing
sequencing multiplexing demultiplexing bam cram sam fastq barcode tag tagging classifiers autocomplete robust
Language:C++ 23
quinlan-lab / hts-python
pythonic wrapper for htslib
genomics htslib python bioinformatics bam sam
Language:Python 23
showteeth / scfetch
Access and Format Single-cell RNA-seq Datasets from Public Resources
geo single-cell-rna-seq zenodo panglaodb ucsc-cell-browser bam fastq format-conversion-tool human-cell-atlas sra cellxgene
Language:R 22
sigven / cacao
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
cancer-genomics sequencing coverage-report sequencing-coverage clinical-decision-support next-generation-sequencing command-line-tool bam alignment cancer pathogenic-loci pathogenic-variants quality-assurance quality-control
Language:R 21
NTU-CCA / EE7207
EE7207 Neural & Fuzzy Systems
rnn rbf svm multi-layer-perceptron som fuzzy-logic fuzzy-modeling fuzzy-identification bam
Language:Python 20