maragkakislab / samql
SQL-like query language for the SAM/BAM file format
☆26Updated last year
Related projects ⓘ
Alternatives and complementary repositories for samql
- RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…☆65Updated last year
- create a gemini-compatible database from a VCF☆56Updated 3 years ago
- deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads☆44Updated 2 years ago
- A method for variant graph genotyping based on exact alignment of k-mers☆87Updated 5 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆33Updated last year
- (WIP) best-practices workflow for rare disease☆58Updated 4 months ago
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Updated 6 years ago
- Long-read splice alignment with high accuracy☆60Updated last month
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆54Updated 7 years ago
- Pipeline for de novo clustering of long transcriptomic reads☆26Updated 2 years ago
- simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.☆44Updated last year
- Bam Read Index - Extract alignments from a bam file by readname☆24Updated 6 months ago
- A set of workflows written in Nextflow for Genome Annotation.☆44Updated 4 months ago
- Retrieve data in genomic intervals with a Python interface for tabix.☆83Updated 7 years ago
- WDL workflows for variant calling and assembly using ONT☆28Updated last month
- A versatile toolkit for k-mers with taxonomic information☆75Updated 3 months ago
- drunk on perbase pileups and lua expressions☆17Updated last year
- A toolkit for annotation of transposable element families from unassembled sequence reads☆31Updated last year
- Genome-wide reconstruction of complex structural variants☆39Updated 2 years ago
- Somatic structural variant caller for long-read data☆47Updated this week
- Tools to annotate genomes using long read transcriptomics data☆45Updated 3 years ago
- Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.☆52Updated last year
- Fast & accurate alignment of barcoded short-reads☆32Updated last year
- A better, faster way to count guides in CRISPR screens.☆27Updated last month
- CRyPTIC data processing pipelines☆31Updated 3 months ago
- gia: Genomic Interval Arithmetic☆51Updated 2 months ago
- Python bindings to minimap2☆16Updated 7 years ago
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆45Updated 2 weeks ago
- Query language for filtering SAM/BAM reads☆31Updated 3 weeks ago
- a wee tool for random access into BGZF files.☆84Updated 6 years ago