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Table of Contents
Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
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.
Sequence (b)uilding information.
(k)-mer table construction.
Show every (m)ismatch.
-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.
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