Version Differences for ALLPATHS-LG Data
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(→100X)
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(→R. sphaeroides)
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| Line 70: | |||
| Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of two circular chromosomes of 3,188,609 bp and 943,016 bp, and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively. | Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of two circular chromosomes of 3,188,609 bp and 943,016 bp, and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively. | ||
| + | ==Website data== | ||
| + | The Illumina and pacbio data were downloaded from [ftp://ftp.broadinstitute.org/pub/papers/assembly/Ribeiro2012/data/ecoli_data_alt.tar.gz ALLPATHS-LG website] <br> | ||
| + | ===Fragment library=== | ||
| + | Reads length : 101bp <br> | ||
| + | Reads amount : 1186190 X2 <br> | ||
| + | Insert size : 180bp <br> | ||
| + | Coverage : 46.02X | ||
| + | ===Jumping library 1=== | ||
| + | Reads length : 93bp <br> | ||
| + | Reads amount : 1615702 X2 <br> | ||
| + | Insert size : 3000bp <br> | ||
| + | ===Jumping library 2=== | ||
| + | Reads length : 93bp <br> | ||
| + | Reads amount : 362199 X2 <br> | ||
| + | Insert size : 3000bp <br> | ||
| + | ===PacBio reads=== | ||
| + | Reads average length : 1514.24bp <br> | ||
| + | Reads amount : 409304 <br> | ||
| + | Coverage : 133.58X <br> | ||
| + | ==Raw data== | ||
| + | The raw data of website data from Sequence Read Archive (SRA) | ||
| + | ===Fragment library=== | ||
| + | Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX131033 SRX131033] <br> | ||
| + | Reads length : 101bp <br> | ||
| + | Reads amount : 13457571 X2 <br> | ||
| + | Insert size : 180bp <br> | ||
| + | Coverage : 522.1X <br> | ||
| + | ===Jumping library 1=== | ||
| + | Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX117481 SRX117481] <br> | ||
| + | ===Jumping library 2=== | ||
| + | Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX145082 SRR492488] <br> | ||
| + | |||
| + | ===PacBio reads=== | ||
| + | Accession : [http://www.ncbi.nlm.nih.gov/sra/SRX109917 SRX109917] [http://www.ncbi.nlm.nih.gov/sra/SRX109901 SRX109901](SRR386913, SRR387092, SRR386907, SRR387035) [http://www.ncbi.nlm.nih.gov/sra/SRX109936 SRX109936] | ||
| + | ==Self-fraction data== | ||
| + | We randomly selected the same fraction as website data from fragment library of raw data by prepare.sh. | ||
| + | PrepareAllPathsInputs.pl\ | ||
| + | DATA_DIR=$PWD/test.genome/data\ | ||
| + | PLOIDY=1\ | ||
| + | FRAG_FRAC=0.088\ | ||
| + | IN_GROUPS_CSV=in_groups.csv\ | ||
| + | IN_LIBS_CSV=in_libs.csv\ | ||
| + | OVERWRITE=True\ | ||
| + | | tee prepare.out | ||
| + | ==100X== | ||
| + | We randomly selected 100X coverage data from fragment library of raw data by prepare.sh. | ||
| + | insert size = 180bp <br> | ||
| + | SRR447685 single end = 13,457,571 reads <br> | ||
| + | Total coverage = (13457571*180/4639675) = 522.0975 <br> | ||
| + | Fraction = 100 / 522.0975 = 0.192 <br> | ||
| + | PrepareAllPathsInputs.pl\ | ||
| + | DATA_DIR=$PWD/test.genome/data\ | ||
| + | PLOIDY=1\ | ||
| + | FRAG_FRAC=0.192\ | ||
| + | IN_GROUPS_CSV=in_groups.csv\ | ||
| + | IN_LIBS_CSV=in_libs.csv\ | ||
| + | OVERWRITE=True\ | ||
| + | | tee prepare.out | ||
| =S. pneumoniae= | =S. pneumoniae= | ||
| Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length. | Streptococcus pneumoniae TIGR4. The S. pneumoniae TIGR4 consists of a circular chromosome of 2,160,842 bp in length. | ||