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Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Restrictions / License Information

No restrictions

Running Instructions

Usage: pandaseq -f forward.fastq -r reverse.fastq [-C module1 -C module2 ...] [-d flags] [-k kmers] [-F] [-g log.txt] [-G log.txt.bz2] [-T threads] [-w output.fasta] [-W output.fasta.bz2] [-6] [-B] [-L length] [-N] [-a] [-j] [-l length] [-o length] [-p primer] [-q primer] [-t threshold] [-u unaligned.txt]
        -C module       Load a sequence validation module.
        -d flags        Control the logging messages. Capital to enable; small to disable.
                (R)econstruction detail.
                Sequence (b)uilding information.
                (F)ile processing.
                (k)-mer table construction.
                Show every (m)ismatch.
                Optional (s)tatistics.
        -k kmers        The number of k-mers in the table.
        -F      Output FASTQ instead of FASTA.
        -g log.txt      Output log to a text file.
        -G log.txt.bz2  Output log to a BZip2-compressed text file.
        -T thread       Run with a number of parallel threads.
        -w output.fasta Output seqences to a FASTA (or FASTQ) file.
        -W output.fasta.bz2     Output seqences to a BZip2-compressed FASTA (or FASTQ) file.
        -6      Use PHRED+64 (CASAVA 1.3-1.7) instead of PHRED+33 (CASAVA 1.8+).
        -B      Allow unbarcoded sequences (try this for BADID errors).
        -L length       Maximum length for a sequence.
        -N      Eliminate all sequences with unknown nucleotides in the output.
        -a      Strip the primers after assembly, rather than before.
        -f forward.fastq        Input FASTQ file containing forward reads.
        -j      Input files are bzipped.
        -l length       Minimum length for a sequence.
        -o length       Minumum overlap region length for a sequence.
        -p primer       Forward primer sequence or number of bases to be removed.
        -q primer       Reverse primer sequence or number of bases to be removed.
        -r reverse.fastq        Input FASTQ file containing reverse reads.
        -t threshold    The minimum probability that a sequence must have to match a primer.
        -u unaligned.txt        File to write unalignable read pairs.

Updated 2014-01-14

System Bugaboo
Version 2.5.0