Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.
Trimmomatic: A flexible read trimming tool for Illumina NGS data
HMMER: biosequence analysis using profile hidden Markov models
The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences.
cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
A single molecule sequence assembler for genomes large and small.
