FLiCK - Format LeveragIng Compression frameworK

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

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

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

Various scripts for working with NGS data in file formats such as VCF, BAM/SAM, and JSON

This repository streamlines the conversion of raw DNA sequencing data from FASTQ to BAM format, incorporating scripts that not only facilitate BAM conversion but also generate Sequence Alignment Map (SAM) files.

htslib for the zig build system

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

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

script to convert bam2cram and reverse using find and samtools

Udo Stenzel's biohazard-tools — a collection of command-line utilities for bioinformatics [MIRROR]

A comprehensive quality check tool for BAM file produced in NGS workflow.

Download fastqs or supplementary files from GEO and upload to hca-util bucket

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)

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.

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

Perl scripts for generating quality control stats from BAM files

A python package storing different tools for different NGS operations

Filter alignments on sequence length and/or identity of first nucleotide.

N mask BAM file according to BED regions