Furnishes functions to control quality for high throughput sequence data. FastQC aims to provide a simple manner to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which users can employ to obtain a quick impression of whether data has any problems of which users should be aware before doing any further analysis.
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Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).
Assists users with DNA sequence analysis. Sequencher is a graphical application that integrates the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. It can generate unique data visualizations using customized plots and graphs that produces ready-to-print graphs. This model also includes an extensive Sanger analysis features.
Enables users to work with high-throughput sequencing data. HTSeq is a program that simplifies development of scripts for processing and analyzing high-throughput sequencing (HTS) data. It contains parsers for common file formats for a variety of types of input data and is suitable as a general platform for a diverse range of tasks.
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Discover our proposed protocols.
They are easy to use or edit to meet your needs.
They are easy to use or edit to meet your needs.
Trimming of sequence reads alters RNA Seq gene expression estimates
Tools (3):
SolexaQA, TopHat, Cufflinks
Topics (15):
CAGE analysis, scRNA-seq analysis, DNase-seq analysis, Ribo-seq analysis, WGS analysis, WES analysis, De novo sequencing analysis, Metatranscriptomic sequencing analysis, RNA-seq analysis, sRNA-seq analysis, ChIP-seq analysis, Metagenomic sequencing analysis, CLIP-seq analysis, Amplicon sequencing analysis, RAD-seq analysis
Draft Genome Sequences of Thermophiles Isolated from Yates Shaft, a Deep Subsurface Environment
Tools (3):
NGS QC Toolkit, MaSuRCA, RAST
Topics (1):
De novo sequencing analysis
Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata
Tools (7):
FastQC, Trimmomatic, CD-HIT, BLASTX, Blast2GO, Bowtie, DESeq2
Topics (4):
sRNA-seq analysis, Metagenomic sequencing analysis, Metatranscriptomic sequencing analysis, RNA-seq analysis
Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk
Tools (3):
skewer, FASTX-Toolkit, STAR
Topics (22):
CAGE analysis, scRNA-seq analysis, DNase-seq analysis, Ribo-seq analysis, WGS analysis, WES analysis, De novo sequencing analysis, RNA-seq analysis, ChIP-seq analysis, sRNA-seq analysis, Metatranscriptomic sequencing analysis, Metagenomic sequencing analysis, CLIP-seq analysis, Amplicon sequencing analysis, GBS analysis, RAD-seq analysis, Rep-seq analysis, Saccharomyces cerevisiae, Homo sapiens, Tooth Demineralization, Hydroxides, Ions
Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297
Tools (3):
FASTX-Toolkit, Velvet, RAST
Topics (3):
De novo sequencing analysis, Fatty Alcohols, Butanols