Converts a SAM or BAM file to FASTQ. This tool extracts read sequences and base quality scores from the input SAM/BAM file and outputs them in FASTQ format. This can be used by way of a pipe to run BWA MEM on unmapped BAM (uBAM) files efficiently.

samtofastq

http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq

released

SamToFastq

processing pipelines

Spliced Transcripts Alignment to a Reference © Alexander Dobin, 2009-2024

star

doi:10.1093/bioinformatics/bts635, PMCID:PMC3530905, PMID:23104886

https://github.com/alexdobin/STAR

released

STAR

processing pipelines

This utility adds the following information that is lost when realigning BAM files:Copies the "read fails platform/vendor quality checks" flag (0x200) from the original BAM;Adds a read group ID to each read based on the read ID, in the format RG:Z:xxxxx.x

bamsync

https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq/bamsync

released

bamsync

processing pipelines

RNA-SeQC 2, an efficient reimplementation of RNA-SeQC (DeLuca et al., 2012) that adds multiple metrics designed to characterize sample quality across a wide range of RNA-seq protocols.

rna-seqc

doi:10.1093/bioinformatics/btab135, PMCID:PMC8479667, PMID:33677499

https://github.com/getzlab/rnaseqc

released

RNA-SeQC

processing pipelines

A quality control tool for high throughput sequence data.

fastqc

https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

released

FastQC

processing pipelines

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

rsem

http://deweylab.github.io/RSEM/

released

RSEM

processing pipelines

Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

picardmarkduplicates

https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates

released

Picard MarkDuplicates

processing pipelines