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shred_seq
Martin Asser Hansen edited this page Oct 2, 2015
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shred_seq shred sequences into random subsequences of a specied length until a specified coverage is reached. The subsequences are alterately derived from the + and - strands.
This is useful for generating artificial reads from contigs for use with different assembly software.
... | shred_seq [options]
[-? | --help] # Print full usage description.
[-s <uint> | --size=<uint>] # Size of subsequences - Default=500
[-c <uint> | --coverage=<uint>] # Coverage to reach - Default=100
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following FASTA entry in the file test.fna
>test
ATGCACATTCGACTAGCA
To read the sequence use read_fasta using the -s switch to
chose subsequences of size of 10 and -c to specify a coverage of 2:
read_fasta -i test.fna | shred_seq -s 10 -c 2
SEQ_NAME: test
SEQ: TGCACATTCG
SEQ_LEN: 10
---
SEQ_NAME: test
SEQ: GCTAGTCGAA
SEQ_LEN: 10
---
SEQ_NAME: test
SEQ: TTCGACTAGC
SEQ_LEN: 10
---
SEQ_NAME: test
SEQ: TCGAATGTGC
SEQ_LEN: 10
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
January 2011
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
shred_seq is part of the Biopieces framework.