---
name: "illuminapairedend"
section: "1"
platform: "linux"
package: "obitools"
version: "1.2.12+dfsg-2"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/illuminapairedend"
---

# illuminapairedend(1)

description of illuminapairedend IMPORTANT: illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform. The program uses as input one or two fastq sequences reads files. illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.

## NAME

illuminapairedend - description of illuminapairedend

**IMPORTANT:**

*illuminapairedend* replaces **solexapairend**.

*illuminapairedend* aims at aligning the two reads of a pair-end library sequenced  using an Illumina platform.

- •

  If the two reads overlap, it returns the consensus sequence together with its quality

- •

  Otherwise, it concatenates sequence merging the forward read and  the reversed-complemented reverse read.

The program uses as input one or two fastq sequences reads files.

- •

  If two files are used one of them must be specified using the **-r** option.  Sequence records corresponding to the same read pair must be in the same order  in the two files.

- •

  If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.

*illuminapairedend* align the forward sequence record with the reverse complement of the  reverse sequence record. The alignment algorithm takes into account the base qualities.

*Example:*

```
> illuminapairedend -r seq3P.fastq seq5P.fastq > seq.fastq
```

The **seq5P.fastq** sequence file contains the forward sequence records. The **seq3P.fastq** sequence file contains the reverse sequence records. Pairs of reads are aligned together and the consensus sequence is stored in the \`\` seq.fastq\`\` file.

## ILLUMINAPAIREDEND SPECIFIC OPTIONS

- **-r \<FILENAME\>, --reverse-reads=\<FILENAME\>**

  Filename points to the file containing the reverse reads.

- **--index-file=\<FILENAME\>**

  - **Filename points to the file containing the illumina index reads**

  - **--score-min=\<FLOAT\>**

  minimum score for keeping alignment. If the alignment score is below this threshold both the sequences are just concatenated. The **mode** attribute is set to the value **joined**.

## OPTIONS TO SPECIFY INPUT FORMAT

### Fastq related format

- **--sanger**

  Input file is in Sanger fastq nucleic format  (standard fastq used by HiSeq/MiSeq sequencers).

- **--solexa**

  Input file is in fastq nucleic format produced by Solexa (Ga IIx) sequencers.

## OPTIONS TO SPECIFY OUTPUT FORMAT

### Standard output format

- **--fasta-output**

  Output sequences in **OBITools** fasta format

- **--fastq-output**

  Output sequences in Sanger fastq format

### Generating an ecoPCR database

- **--ecopcrdb-output=\<PREFIX\_FILENAME\>**

  Creates an ecoPCR database from sequence records results

### Miscellaneous option

- **--uppercase**

  Print sequences in upper case (default is lower case)

## COMMON OPTIONS

- **-h, --help**

  Shows this help message and exits.

- **--DEBUG**

  Sets logging in debug mode.

## ILLUMINAPAIREDEND ADDED SEQUENCE ATTRIBUTES

- •

  ali\_dir

- •

  ali\_length

- •

  score

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  score\_norm

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  mode

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  pairend\_limit

- •

  sminL

- •

  sminR

- •

  seq\_ab\_match

- •

  seq\_a\_single

- •

  seq\_b\_single

- •

  seq\_a\_mismatch

- •

  seq\_b\_mismatch

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  seq\_a\_deletion

- •

  seq\_b\_deletion

- •

  seq\_b\_insertion

- •

  seq\_a\_insertion

## AUTHOR

The OBITools Development Team - LECA

## COPYRIGHT

2019 - 2015, OBITool Development Team