2021 The Basic Alignment Workflow - Core NGS Tools - UT Austin Wikis
3. Day 2: Introduction to basic NGS pipelines — CODATA-RDA Research Data Science Advanced Workshop on Bioinformatics 1.0 documentation
gatk/doc_archive/deprecated/[How_to]_Generate_a_BAM_for_variant_discovery_(long).md at master · broadgsa/gatk · GitHub
BRB-SeqTools
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads | Scientific Reports
Convert Dante Labs / Nebula (BAM / CRAM / FASTQ) to RAW format - DNAGenics
SeqShop: Sequence Mapping and Assembly Practical, December 2014 - Genome Analysis Wiki
Data Files
Overview of widely used sequencing formats. Usually, sequencers... | Download Scientific Diagram
How to Map and clean up short read sequence data efficiently - Legacy GATK Forum
GitHub - PacificBiosciences/bam2fastx: Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.
BAM Tools
Wrangling Genomics
Samtools: Easy Converting of BAM to FASTA and FASTQ
Why do I not see any FASTQs (or incomplete FASTQs) for the SRA of my interest? – 10X Genomics
Low mapping rate 6 - Converting sorted BAM to FASTQ — What do you mean "heterogeneity"?
BAM Tools
seqtools – McDonald Lab
FASTQ AND BAM PROCESSING OVERVIEW - NVIDIA Docs
Wrangling Genomics
How to Generate an unmapped BAM from FASTQ or aligned BAM - Legacy GATK Forum
WGS Data Types & Sizes and Runtimes
oldIntroduction to ChIP-seq | crc.pitt.edu | University of Pittsburgh
SeqShop: Sequence Mapping and Assembly Practical, December 2014 - Genome Analysis Wiki
Parsing and analyzing BAM files
FastQ Format – NGS Analysis
Convert from BAM to fastq - usegalaxy.org support - Galaxy Community Help
