Mcschatz: Created page with 'dumpreads extracts reads from a bank and reports them in fasta or fastq format .USAGE. dumpreads [options] .DESCRIPTION. Takes an AMOS bank directory …'

2011-04-14T22:41:17Z

Created page with 'dumpreads extracts reads from a bank and reports them in fasta or fastq format .USAGE. dumpreads [options] <bank path> .DESCRIPTION. Takes an AMOS bank directory …'

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dumpreads extracts reads from a bank and reports them in fasta or fastq format

.USAGE.
dumpreads [options] <bank path>

.DESCRIPTION.
Takes an AMOS bank directory and dumps selected reads to
stdout in FASTA or FASTQ format.

.OPTIONS.
-f Dump reads in fastq format
-Q int Use this as the min base quality (default: 33 / Sanger FASTQ)
-q Dump qualities in fasta format instead of sequence
-e Use EIDs for FastA header instead of IIDs
-r Ignore clear range and dump entire sequence
-c Display clear range information on FASTA header for TIGR Assembler
-E file Dump just the eids listed in file
-I file Dump just the iids listed in file
-L num Set the maximum number of bases per line (Default: 70)
-m num Minimum IID to display (not included) (Default all; not compatible with -e,-E,-I options)
-M num Maximum IID to display (included) (Default all; not compatible with -e,-E,-I options)
-h Display help information
-s Disregard bank locks and write permissions (spy mode)
-v Display the compatible bank version

.KEYWORDS.
amos bank, reads, converters

Dumpreads - Revision history

Mcschatz: Created page with 'dumpreads extracts reads from a bank and reports them in fasta or fastq format .USAGE. dumpreads [options] .DESCRIPTION. Takes an AMOS bank directory …'