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r_for_biologists

Scripts and data for Plotting in R for Biologists, a video course on YouTube

r_seq

R scripts for NGS data analysis

salsa

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

sambamba

Tools for working with SAM/BAM/CRAM data

samtools

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

san_zi_jing

sandbox

Primordial soup of short scripts

scallop

Scallop is a reference-based transcriptome assembler for RNA-seq

scripts

Scripts to handle NGS data and other biological data

scripts-1

scrna.seq.course

Analysis of single cell RNA-seq data course

scythe

A 3'-end adapter contaminant trimmer

seqtk

Toolkit for processing sequences in FASTA/Q formats

sequelqc

PacBio quality check program specifically for Sequel platform

shinycircos

an R/shiny application for creation of Circos plot interactively

silk-v3-decoder

[Skype Silk Codec SDK]Decode silk v3 audio files (like wechat amr, aud files, qq slk files) and convert to other format (like mp3). Batch conversion support.

simple-consensus-per-read-group

Generate a simple consensus using % identity thresholds and minimum coverage from a SAM/BAM file, treating each read group (RG) separately.

simplest_mediadata_test

samples to handling multimedia data

sjm

Simple Job Manager

sjoye.github.io

sjtu-courses

上海交通大学课程资料分享

smartdenovo

Ultra-fast de novo assembler using long noisy reads

smcpp

SMC++ infers population history from whole-genome sequence data.

smrt-analysis

SMRT® Analysis is PacBio's bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data

smrt-link

SMRT® Link is the web-based end-to-end workflow manager for the Sequel™ System.

smrtflow

SMRT Link and Analysis Server, PacBio Scala analysis tools and Common models

smrtlinkr

R package to interface with SMRTLink REST API

snpgenie

Perl software for estimating evolutionary parameters from pooled next-generation sequencing SNP data

snphylo

A pipeline to generate a phylogenetic tree from huge SNP data

soapdenovo2

Next generation sequencing reads de novo assembler.