GitHub topics: cram

Repositories

samtools/htsjdk

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

Language: Java - Size: 164 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 286 - Forks: 243

samtools/htslib

C library for high-throughput sequencing data formats

Language: C - Size: 12.4 MB - Last synced at: 3 days ago - Pushed at: 12 days ago - Stars: 848 - Forks: 448

ag-sc/CRAM-Generation-LLM

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

Language: Python - Size: 19.5 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 4 - Forks: 1

gregzanch/cram

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

Language: TypeScript - Size: 118 MB - Last synced at: 4 days ago - Pushed at: about 2 years ago - Stars: 52 - Forks: 5

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: 1.05 GB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 165 - Forks: 14

prysk/prysk Fork of aiiie/cram

Functional tests for command line applications

Language: Python - Size: 1.93 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 11

chrovis/cljam

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

Language: Clojure - Size: 35.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 90 - Forks: 13

nf-cmgg/smallvariants

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

Language: Nextflow - Size: 10.5 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 8 - Forks: 1

beling/impartial-games

Rust software for solving impartial games.

Language: Rust - Size: 197 KB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 4 - Forks: 0

biosails/pheniqs

Fast and accurate sequence demultiplexing

Language: C++ - Size: 72.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 4

maurya-anand/getBamDepth

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

Language: Perl - Size: 1.43 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

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

Language: Nextflow - Size: 5.37 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 19 - Forks: 2

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).

Language: Python - Size: 258 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 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.

Language: Python - Size: 15.1 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 1