bionitio-team / bionitio-python
Demonstrating best practices for bioinformatics command line tools
☆26Updated 4 years ago
Related projects ⓘ
Alternatives and complementary repositories for bionitio-python
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆43Updated 2 years ago
- overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites☆28Updated this week
- Samwell: a python package for using genomic files... well☆19Updated 2 years ago
- A template repository for Snakemake pipepline(s) and a python command-line toolkit.☆27Updated last month
- Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.☆38Updated last year
- The Zavolab Automated RNA-seq Pipeline☆35Updated 3 weeks ago
- Simplify snpEff annotations for interesting cases☆21Updated 5 years ago
- ☆21Updated last year
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆41Updated 2 years ago
- v2.x of the microassembly based somatic variant caller☆14Updated 2 months ago
- Structural variant pipeline☆17Updated 4 years ago
- Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer☆21Updated 3 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated last year
- filtering trio-based genetic variants in VCFs for clinical review☆20Updated 4 years ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Updated 2 years ago
- ☆13Updated 7 years ago
- Making Snakemake workflows into full-fledged command line tools since 1999.☆51Updated 6 years ago
- Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.☆19Updated 2 years ago
- pathoscore evaluates variant pathogenicity tools and scores.☆21Updated 2 years ago
- BigWig manpulation tools using libBigWig and htslib☆28Updated 3 months ago
- Structural Variant Prediction Viewer☆31Updated 7 years ago
- Ximmer is a system for CNV calling on exome and targeted genomic sequencing☆19Updated 3 months ago
- Python bindings for the TaxonKit library☆31Updated 3 months ago
- Nextflow workshop 2018 -- Training pages -> https://nextflow-io.github.io/nf-hack18/☆18Updated 5 years ago
- Hybridization probe design for targeted genomic sequencing of diverse and hypervariable viral taxa☆21Updated last year
- Using k-mers to call HLA alleles in RNA sequencing data☆22Updated 6 years ago
- Please consider using/contributing to https://github.com/nf-core/sarek☆40Updated 3 years ago
- a Shiny/R application to view and annotate copy number variations☆28Updated last year
- BED QC tool (in the making)☆15Updated 2 years ago
- Variant catalogue pipeline☆25Updated this week