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.
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
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.
A single molecule sequence assembler for genomes large and small.
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
