Bastien
Chevreux
bach@chevreux.org

> Solomon Short

> Rome didn't fall in a day either.

# Preparing data

## Introduction

Most of this chapter and many sections are just stubs at the moment.

## Sanger

Outside MIRA: transform .ab1 to .scf, perform sequencing vector clip (and cloning vector clip if used), basic quality clips.

Recommended program: `gap4` (or rather `pregap4`) from the Staden 4 package.

## Roche / 454

Outside MIRA: convert SFF instrument from Roche to FASTQ, use `sff_extract` for that. In case you used "non-standard" sequencing procedures: clip away MIDs, clip away non-standard sequencing adaptors used in that project.

## Illumina

Outside MIRA: for heavens' sake: do NOT try to clip or trim by quality yourself. Do NOT try to remove standard sequencing adaptors yourself. Just leave Illumina data alone! (really, I mean it).

MIRA is much, much better at that job than you will probably ever get ... and I dare to say that MIRA is better at that job than 99% of all clipping/trimming software existing out there. Just make sure you use the -CL:pec (proposed_end_clip) option of MIRA.

The only exception to the above is if you (or your sequencing provider) used decidedly non-standard sequencing adaptors. Then it might be worthwhile to perform own adaptor clipping. But this will not be the case for 99% of all sequencing projects out there.

Joining paired-ends: if you want to do this, feel free to use any tool which is out there (TODO: quick list). Just make sure they do not join on very short overlaps. For me, the minimum overlap is at least 17 bases.

## Pacific Biosciences

Outside MIRA: MIRA needs error corrected reads, either

- PacBio CCS reads (circular consensus sequence) which you get from the PacBio SMRTAnalysis pipeline
- or self-corrected or reads corrected with other sequencing technologies which you will get either from the PacBio HGAP pipeline or the pacbioToCA pipeline

Assembly of uncorrected PacBio reads (CLR) is currently not supported officially as of MIRA 4.0.

## Ion Torrent

Outside MIRA: need to convert BAM to FASTQ. Need to clip away non-standard sequencing adaptors if used in that project. Apart from that: leave the data alone.