archive:bioinformatic_tools:gs_de_novo_assembler
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archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/24 15:48] karplus Put -rst 0 back in, with explanation |
archive:bioinformatic_tools:gs_de_novo_assembler [2010/05/28 22:30] jstjohn |
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| Note: earlier versions of Newbler provided serially numbered contigs, but version 2.3 seems to skip numbers rather arbitrarily, so that the range of the numbers is larger than the size of the set of contigs. Look at the counts (in assembly/454NewblerMetrics.txt) or run a program to count the contigs, rather than relying on the largest contig number. | Note: earlier versions of Newbler provided serially numbered contigs, but version 2.3 seems to skip numbers rather arbitrarily, so that the range of the numbers is larger than the size of the set of contigs. Look at the counts (in assembly/454NewblerMetrics.txt) or run a program to count the contigs, rather than relying on the largest contig number. | ||
| + | |||
| + | For large genomes you can pass the -large argument to runProject and it will take some time-saving shortcuts. | ||
| + | <code> | ||
| + | ${BIN}/newAssembly . | ||
| + | ${BIN}/addRun . ${SFFS_IN} | ||
| + | ${BIN}/addRun . ${FA_IN} | ||
| + | ${BIN}/runProject -e ${EXPECTED_COVERAGE} -large -rst 0 -noace . | ||
| + | </code> | ||
| == Mapping to existing genome == | == Mapping to existing genome == | ||
archive/bioinformatic_tools/gs_de_novo_assembler.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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