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
GENSCAN is a general-purpose gene identification program
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.
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
cutadapt removes adapter sequences fromnhigh-throughput sequencing data. This is usually necessary when the readnlength of the sequencing machine is longer than the molecule that isnsequenced, for example when sequencing microRNAs.
A single molecule sequence assembler for genomes large and small.
