Development of our tool was driven by real molecular-biology issues poisoning 454 and IonTorrent data
There is no other 454 adapter trimming tool looking for real issues.
We can at least rescue part of the deemed low-qual sequence to make the final sequence longer.
Not always is the sequencer or vendor to be blamed.
We can remove the offending adapters/MIDs/artefacts from your reads.
Unremoved adapters prevent contig joining and scaffolding.
Sometimes you could gain even 200nt of perfectly usable sequence.
In overall, minimize assembly artefacts, make the assembly feasible and correct.
We learned that from never-ending analyses of >1800 independent sample datasets
Sometimes we can tell you based on the data what you did wrong.
We can compare the results and tell you which was your best trial.
We are fixing bugs still present in software from Roche and IonTorrent.
We can analyze and clean your Roche-454 / IonTorrent / Illumina sequencing data. We improve your assemblies.
We tell you which sample preparation was your best. We tell you what to avoid next time.
For Roche 454 and IonTorrent datasets we offer:
° full quality control of any sequencing data
° distribution of sample insert sizes
° types of sequencing and basecalling errors
° protocol-specific artefacts
° types of adapters used
° just perfect trimming of your reads (remove primers, adapters, Multiplex IDentifiers (MIDs), artefacts)
° determination of overhead of your sample preparation protocol and sequencing
° tuning Roche 454 read high-/low-qual boundaries, rescuing even 250nt of your sample sequence (usually 80 to 160nt);
° performance comparison of your samples or sample preparation procedures to each other
° quantification of 5'- and 3'-ends of transcripts in your sequencing reads, e.g. of (un)directed cDNA preparations
° detection of authentic mRNA polyA-tails thanks to a special approach coping with sequencing errors in homopolymers (and detection of their polyT forms)
° matched sequences are aligned to flow for improved trimming precision
We also clean RNA-seq datasets from Illumina machines based on Evrogen MINT, Clontech SMART protocols, full-length cDNA protocols and some additional less common protocols (unpublished protocols of GATC Biotech, LGC Genomics, BioST, modification of Clontech MINT method as Cap-Trsa-CV, T7 RNApol run-off-based transcripts, ...)