cram

There are 1 repository under cram topic.

• samtools / htslib

  C library for high-throughput sequencing data formats

  bambcfbioinformaticscramhtslibngssamvcf
  Language:C 825

• samtools / htsjdk

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

  genomicssequencingdnangsbamcramsamfastavcfjava-apijava
  Language:Java 286

• 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

  genomicscompressionfastqvcfbamsamfastagvf23andmegzipbgzipsamtoolsbwacram
  Language:C 160

• Griffan / VerifyBamID

  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

  bambioinformaticsbiostatisticscontaminationcramdna-sequencesgeneticsnext-generation-sequencingqc-analysis
  Language:mupad 96

• chrovis / cljam

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

  2bitbambcfbedbigwigbioinformaticsclojurecramfastafastqgenomicsgffsamvcfwig
  Language:Clojure 89

• sbslee / fuc

  Frequently used commands in bioinformatics

  vcfbedfastqbioinformaticsapiclibamsamcrammafvisualizationfastagffgtf
  Language:Python 53
• cram

  gregzanch / cram

  cram is a computational room acoustics module to simulate and explore various acoustic properties of a modeled space

  raytraceracousticssimulationfdtdimage-source-modelroom-acousticsroom-impulse-responsecomputational-acousticsray-tracingwebappcram
  Language:TypeScript 45

• ncherric / Iliad

  ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

  automaticgeneticsgenomics-datasnakemakeworkflowbioinformaticsfastqgenomicsmodularizationcramidatvcf
  Language:Python 28

• prysk / prysk

  Functional tests for command line applications

  cramclifunctional-testingsnapshot-testingcli-testingpryskhacktoberfest
  Language:Python 28

• biosails / pheniqs

  Fast and accurate sequence demultiplexing

  autocompletebambarcodeclassifierscramdemultiplexingfastqmultiplexingrobustsamsequencingtagtagging
  Language:C++ 27

• nf-cmgg / structural

  A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

  annotationcnvcramnextflow-pipelinengsngs-pipelinerepeatsshort-readsstructural-variation
  Language:Nextflow 19

• nf-cmgg / germline

  A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

  annotationcramgenotypinggermlinegermline-variant-callingngsngs-pipelineshort-reads
  Language:Nextflow 8

• brentp / bpbio

  basepair bio: a single binary with many useful genomics subtools.

  genomicsgenomics-visualizationcrambamstructural-variationhigh-throughput-sequencing
  Language:Nim 6

• brentp / bedder-rs

  an API for intersections of genomic data

  bambedbioinformaticscramgenomicsvcf
  Language:Rust 4

• ag-sc / CRAM-Generation-LLM

  Using ChatGPT & GPT-4 to generate CRAM & PyCRAM designators in a one-shot fashion

  cramplan-generationgptllmsaction-similaritypycram
  Language:Python 3

• beling / impartial-games

  Rust software for solving impartial games.

  cgtchompchomp-gamecombinatorial-gamecombinatorial-game-theorycramgame-treegame-tree-searchgrundyimpartial-gamesmexsolversolversspraguetransposition-table
  Language:Rust 3

• 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).

  bamcramgenomicsmosaicsamvcf
  Language:Python 1

• 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.

  bamcramgenomicssamtumorizedvcf
  Language:Python 1

• machinekoder / Fabrikator-Mini-CRAMPS

  Machinekit configuration for the Fabrikator Mini + CRAMPS board

  machinekit-configurationcram3d-printingmachinekitfabrikator-minitinyboy
  Language:Python 1

• maurya-anand / getBamDepth

  A script to report depth of coverage from BAM/SAM/CRAM file or parse the output generated from "samtools depth"

  bamcoveragengssamtoolscramsam
  Language:Perl 1

• REGOVAR / Pirus

  a REST service to launch pipeline

  bampipelinebioinformaticscramvariantsgenetics
  Language:Python 1

• mtso / cram

  Line cramming/un-cramming utility

  cramuncrampackermangle
  Language:Go

• nikolausschueler / tapconverters

  Convert output from Cram (and some other tools) to TAP (Test Anything Protocol)

  pythoncramtesting-toolsvagrantvagrantfile
  Language:Python