PCR primer design

Primer3Plus: Picks primers from a DNA sequence

PCR primer design

Primer-Blast: Tool for finding primers specific to PCR template

PCR primer design

OligoEvaluator™: The most powerful and comprehensive package to analyze DNA oligo to successful PCR

PCR primer design

Multiple Primer Analyzer: For analyzing and comparing multiple primer sequences simultaneously such as self and cross dimer analysis and TM calculate

PCR primer design

Oligo Calc: Oligonucleotide Properties Calculator

Database

GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences

Database

ViPR: Virus Pathogen Database and Analysis Resource

Database

Monocots PLAZA 4.5 : comparative genomics in plants for monocots

Denovo assembly

IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads

Denovo assembly

ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.

RNAseq read QC

AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

RNAseq read QC

FastP: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

RNAseq read QC

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.