illuminapairedend1
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.
Options
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-r <FILENAME>, --reverse-reads=<FILENAME> -
Filename points to the file containing the reverse reads.
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--index-file=<FILENAME>
- Filename points to the file containing the illumina index reads
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--score-min=<FLOAT> -
minimum score for keeping alignment. If the alignment score is below this threshold both the sequences are just concatenated. The
modeattribute is set to the valuejoined.
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
OBIToolsfasta 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)
Options
-
-h, --help -
Shows this help message and exits.
-
--DEBUG -
Sets logging in debug mode.
Illuminapairedend added sequence attributes
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ali_dir |
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ali_length |
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score |
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score_norm |
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mode |
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pairend_limit |
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sminL |
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sminR |
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seq_ab_match |
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seq_a_single |
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seq_b_single |
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seq_a_mismatch |
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seq_b_mismatch |
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seq_a_deletion |
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seq_b_deletion |
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seq_b_insertion |
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seq_a_insertion |