Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file

Visualize your BAM alignments with Circos

Pipeline for copy number variant calling from Whole Exome sequencing data using CODEX

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

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

Split a BAM file by haplotype support

FLiCK - Format LeveragIng Compression frameworK

A Python3 script to quickly spot check 10 random sequences from a BAM/FASTx file.

Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]

Alter or Add Read Group Tags to BAM Files

Hilbert Mapper is a C++ implementation of Hilbert's space filling curve to represent read coverage on genomic sequences. Although it can be used to represent any unidimensional vector of positive numerical data.

Udo Stenzel’s jivebunny — a probabilistic demultiplexer for Illumina sequencing data [MIRROR]

COverage Analysis Tool have been developed in 2016. It aims to automatically find bad quality regions of coding sequences in a set of sequencing data. It includes a graphical interface.

Perl scripts for generating quality control stats from BAM files

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

Docker based on bioconda distribution (v.1.23), with fixed memory issue

SAMtools and BCFtools (v1.10) for manipulating next-generation sequencing data, from bioconda

This Roddy plugin contains a basic bam to fastq workflow using Picard and Samtools.