archive:bioinformatic_tools:soapdenovo
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archive:bioinformatic_tools:soapdenovo [2010/05/02 20:54] galt |
archive:bioinformatic_tools:soapdenovo [2015/07/28 06:26] (current) ceisenhart ↷ Page moved from bioinformatic_tools:soapdenovo to archive:bioinformatic_tools:soapdenovo |
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| Can use a hierarchy of sizes of paired-end data.\\ | Can use a hierarchy of sizes of paired-end data.\\ | ||
| Has been successfully used to sequence the Panda and Human genomes.\\ | Has been successfully used to sequence the Panda and Human genomes.\\ | ||
| - | Quality seems good. They ran Panda genome on 256GB workstation with 32 CPUs. | + | Quality seems good. They ran Panda genome on 512GB workstation with 32 CPUs. |
| There is a [[http://soap.genomics.org.cn/soapdenovo.html|description]] which contains a | There is a [[http://soap.genomics.org.cn/soapdenovo.html|description]] which contains a | ||
| Line 25: | Line 25: | ||
| Downloaded the binaries for SOAPdenovo and [[http://soap.genomics.org.cn/about.html#resource2|GapCloser]]. I copied these binaries to the /bin folder since there are only two, and they at least correctly display a help message when you run them without arguments. | Downloaded the binaries for SOAPdenovo and [[http://soap.genomics.org.cn/about.html#resource2|GapCloser]]. I copied these binaries to the /bin folder since there are only two, and they at least correctly display a help message when you run them without arguments. | ||
| + | |||
| + | ==== Method ==== | ||
| + | The method for SOAPdenovo is described in the paper [[http://genome.cshlp.org/content/20/2/265.full|"De novo assembly of human genomes with massively parallel short read sequencing"]] by Li et al. | ||
| + | |||
| + | === Short Read Data === | ||
| + | Fragment and paired-end libraries are sequenced using various insert sizes. They used read lengths from 35 to 75 bp and insert sizes of 140 bp, 440 bp, 2.6 kb, 6 kb, and 9.6 kb. | ||
| + | |||
| + | Basic error correction was performed on the reads using K-mer counting to reduce the memory usage when constructing the de Bruijn graph. This was done by identifying low frequency (occurring <3 times) 17-mers and correcting these K-mers to the candidate with the highest frequency. | ||
| + | |||
| + | === De Bruijn Graph === | ||
| + | The next step is to build the de Bruijn graph to represent overlap of k-mers. 25-mers were used in their assembly. | ||
| + | Only the single-end and paired-end reads with short insert sizes (<1 kb) were used in the graph due the high probability of chimeric reads in the long-insert pairs from the circularizing and fragmentation process. Further error correction is done using the de Bruijn graph. | ||
| + | |||
| + | * Clip tips (low coverage paths that lead to dead ends) | ||
| + | * Remove low coverage links | ||
| + | * 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. | ||
| ==== Quirks ==== | ==== Quirks ==== | ||
| Line 38: | 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.1272833650.txt.gz · Last modified: 2010/05/02 20:54 by galt
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