EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
- Sequence analysis
- Next generation sequencing
Working on 454 run with long linkers and random insert orientation, only EMBOSS could help me to produce a clean FASTQ file with orientation corrected and linkers removed. Update: and now it supports SAM format, which is really useful.