biod / sambamba
Tools for working with SAM/BAM data
☆577Updated last month
Alternatives and similar repositories for sambamba:
Users that are interested in sambamba are comparing it to the libraries listed below
- Transcript assembly and quantification for RNA-Seq☆402Updated 3 weeks ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆455Updated 2 weeks ago
- C++ API & command-line toolkit for working with BAM data☆421Updated 6 months ago
- Graph-based alignment (Hierarchical Graph FM index)☆491Updated 2 months ago
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆403Updated 3 weeks ago
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆424Updated 10 months ago
- This Snakemake pipeline implements the GATK best-practices workflow☆245Updated last year
- Plot structural variant signals from many BAMs and CRAMs☆536Updated 6 months ago
- Count bases in BAM/CRAM files☆310Updated 3 years ago
- ☆228Updated 8 months ago
- Haplotype VCF comparison tools☆422Updated last year
- Java utilities for Bioinformatics☆491Updated this week
- annotate a VCF with other VCFs/BEDs/tabixed files☆367Updated last year
- The next version of bwa-mem☆731Updated 5 months ago
- De novo assembler for single molecule sequencing reads using repeat graphs☆803Updated 5 months ago
- ☆261Updated 2 months ago
- Mummer alignment tool☆480Updated this week
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆306Updated 8 months ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆393Updated last month
- parallel fastq-dump wrapper☆286Updated last year
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆380Updated last month
- Bayesian haplotype-based genetic polymorphism discovery and genotyping.☆801Updated 7 months ago
- Reads simulator☆268Updated 3 years ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆712Updated last week
- Tools to process and analyze deep sequencing data.☆692Updated this week
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆208Updated 4 years ago
- This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.☆237Updated 2 years ago
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆261Updated last year
- Strelka2 germline and somatic small variant caller☆363Updated 3 years ago
- BEDOPS: high-performance genomic feature operations☆308Updated last year