Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Scythe is a Bayesian adapter trimmer .
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.
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
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.
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
