Genome browser and variant annotation

microsatellite instability detection using tumor only or paired tumor-normal data

Learning the Sequence Alignment/Map format

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

📇 Retrieve data in genomic intervals with a Python interface for tabix.

Sequence alignment tools

Multi-sample somatic variant caller

⛰ covtobed | Convert the coverage track from a BAM file into a BED file

Go / Golang Bioinformatics Library

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Splice junction analysis and filtering from BAM files

create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

Parse and process SAM and BAM formatted files

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data

vSNP -- validate SNPs

knowledge-based genotyping of cancer hotspots from the tumor BAM files

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Split a BAM file by haplotype support

Utilities for analyzing next generation sequencing data.

Datastores for reads, not your papa's FASTQ files.