Roche/454 software pipeline underestimates basecalling qualities or discards usable sequence for an unknown reason at least (Roche GS FLX+ sequencing)

Although Roche’s adapter- and quality-based trimming results in reads 168nt long on average, reads with an average of up to 511nt could be obtained by more thorough quality analysis (SRR341912_F4EVV7N01)