archive:bioinformatic_tools:soapdenovo
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archive:bioinformatic_tools:soapdenovo [2011/05/18 21:05] svohr |
archive:bioinformatic_tools:soapdenovo [2011/06/08 17:36] svohr |
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| * Remove low coverage links | * Remove low coverage links | ||
| * Resolve tiny repeats greater than K, but less than the read lengths. | * Resolve tiny repeats greater than K, but less than the read lengths. | ||
| - | * Merge bubbles, paths with the same start and end. These can represent an error or a true polymorphism. | + | * Merge bubbles (paths with the same start and end). These can represent an error or a true polymorphism. |
| ==== Quirks ==== | ==== Quirks ==== | ||
| Line 55: | Line 55: | ||
| Perhaps it just won't take the fasta input by itself. | Perhaps it just won't take the fasta input by itself. | ||
| It might work if you include a qual file with your fasta. | It might work if you include a qual file with your fasta. | ||
| + | |||
| + | ==== Using SOAPdenovo ==== | ||
| + | |||
| + | SOAPdenovo has three executables each tuned for a different range of k-mer sizes (SOAPdenovo-31mer, SOAPdenovo-63mer, SOAPdenovo-127mer). For example, ''SOAPdenovo-31mer'' works best on k-mer sizes up to and including 31. For larger k-mers than 31 and lower than 64, use ''SOAPdenovo-63mer''. | ||
| + | |||
| + | SOAPdenovo requires a configuration file that describes the libraries that will be used in the assembly. A library entry is required for each read file or pair of read files in the case of paired-end reads. Here is an example of the 5 library entries for 1 lane of run1. | ||
| + | |||
| + | <code> | ||
| + | [LIB] | ||
| + | #average insert size | ||
| + | avg_ins=150 | ||
| + | |||
| + | #if sequence needs to be reversed | ||
| + | reverse_seq=0 | ||
| + | |||
| + | #in which part(s) the reads are used | ||
| + | asm_flags=3 | ||
| + | |||
| + | #in which order the reads are used while scaffolding | ||
| + | rank=1 | ||
| + | |||
| + | #fastq file for read 1 | ||
| + | q1=/campusdata/BME235/data/slug/clean/run1_seqprep_quake/s_1_1_qseq_seqprep.cor.fastq.gz | ||
| + | #fastq file for read 2 always follows fastq file for read 1 | ||
| + | q2=/campusdata/BME235/data/slug/clean/run1_seqprep_quake/s_1_2_qseq_seqprep.cor.fastq.gz | ||
| + | |||
| + | [LIB] | ||
| + | reverse_seq=0 | ||
| + | asm_flags=3 | ||
| + | rank=1 | ||
| + | q=/campusdata/BME235/data/slug/clean/run1_seqprep_quake/s_1_1_qseq_seqprep.cor_single.fastq.gz | ||
| + | |||
| + | [LIB] | ||
| + | reverse_seq=1 | ||
| + | asm_flags=3 | ||
| + | rank=1 | ||
| + | q=/campusdata/BME235/data/slug/clean/run1_seqprep_quake/s_1_2_qseq_seqprep.cor_single.fastq.gz | ||
| + | |||
| + | [LIB] | ||
| + | reverse_seq=0 | ||
| + | asm_flags=3 | ||
| + | rank=1 | ||
| + | q=/campusdata/BME235/data/slug/clean/run1_seqprep_quake/s_1_merged_qseq_seqprep.cor.fastq.gz | ||
| + | |||
| + | </code> | ||
| + | |||
archive/bioinformatic_tools/soapdenovo.txt · Last modified: 2015/07/28 06:26 by ceisenhart
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