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rapmap

Rapid sensitive and accurate read mapping via quasi-mapping

readfq

Fast multi-line FASTA/Q reader in several programming languages

rebaler

reference-based long read assemblies of bacterial genomes

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

remap

create a map by R

repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

rephasingbins

Scripts for rephasing Bins

reseqtools

A Toolkit for analyzing next-generation DNA Re-Sequencing data

resolving-the-complex-bordetella-pertussis-genome-using-barcoded-nanopore-sequencing

Developing a sequencing pipeline for Bordetella pertussis genomes

rgaat_v2

Add multiple thread function for genome comparison

ria2

Source code for R in Action, Second Edition

rnacocktail

rnaseq-workflow

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rnaseqeval

A tool for evaluating RNA seq mapping

rpkm_rnaseq_count

RPKM for RNASeq counts

rrbs_scp

Steps for RRBS alignment

rrna-ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

rsem_tutorial

A short tutorial on how to use RSEM

s-plot

A simple plot library

sacring

Sub-Assembly of Chloroplast genome from PE RAD-seq

safe-rm

A safe "rm" script which is meant to be used in place of rm system command in linux . This script will safely delete your files and put them in the trash. This solves accidental removals.

sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads

sailfish-cir

a pipeline for quantification of circular RNA.

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

salsa

SALSA: A tool to scaffold long read assemblies with Hi-C data

sam-to-bam

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

sambamba

Tools for working with SAM/BAM data

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data