biod / sambambaLinks
Tools for working with SAM/BAM data
☆595Updated 9 months ago
Alternatives and similar repositories for sambamba
Users that are interested in sambamba are comparing it to the libraries listed below
Sorting:
- C++ API & command-line toolkit for working with BAM data☆429Updated 4 months ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆486Updated last month
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆845Updated 4 months ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆454Updated last year
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆524Updated last month
- Haplotype VCF comparison tools☆445Updated last year
- Graph-based alignment (Hierarchical Graph FM index)☆513Updated last month
- Java utilities for Bioinformatics☆512Updated last month
- Strelka2 germline and somatic small variant caller☆383Updated 3 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆326Updated 4 months ago
- Count bases in BAM/CRAM files☆318Updated 3 years ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆383Updated last month
- Transcript assembly and quantification for RNA-Seq☆464Updated this week
- BEDOPS: high-performance genomic feature operations☆351Updated 5 months ago
- Plot structural variant signals from many BAMs and CRAMs☆552Updated last year
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆432Updated 2 months ago
- Structural variation caller using third generation sequencing☆619Updated last month
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆439Updated 9 months ago
- ☆268Updated last month
- This Snakemake pipeline implements the GATK best-practices workflow☆259Updated 2 years ago
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆506Updated this week
- Structural variant and indel caller for mapped sequencing data☆442Updated 2 years ago
- The next version of bwa-mem☆785Updated 3 months ago
- TransDecoder source☆298Updated last week
- A single molecule sequence assembler for genomes large and small.☆691Updated last month
- An accurate GFF3/GTF lift over pipeline☆507Updated 2 years ago
- Reads simulator☆281Updated 4 years ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆400Updated 2 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆657Updated 3 months ago
- A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.☆537Updated 4 months ago