PCR primer design
Primer3Plus: Picks primers from a DNA sequence
PCR primer design
Oligo Calc: Oligonucleotide Properties Calculator
Database
Monocots PLAZA 4.5 : comparative genomics in plants for monocots
Denovo assembly
Trinity: RNA-Seq De novo Assembly Using Trinity
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.
Gene analysis
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity.
Gene analysis
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Gene analysis
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
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