Mercurial > repos > jjohnson > shear
comparison shear_sv.xml @ 2:b84716da5595
Update to SHEAR v0.2.9
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Sun, 27 Apr 2014 19:57:03 -0500 |
| parents | 3cbbffb3ae47 |
| children | 7506693aff3b |
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| 1:3cbbffb3ae47 | 2:b84716da5595 |
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| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.7"> | 2 <tool id="shear_sv" name="SHEAR-SV" version="0.0.9"> |
| 3 <description>find SVs and estimate the heterogeneity levels from a BAM</description> | 3 <description>find SVs and estimate the heterogeneity levels from a BAM</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="0.2.7">shear</requirement> | 5 <requirement type="package" version="0.2.9">shear</requirement> |
| 6 <requirement type="package" version="0.1.19">samtools</requirement> | 6 <requirement type="package" version="0.1.19">samtools</requirement> |
| 7 <requirement type="package" version="0.6.2">bwa</requirement> | 7 <requirement type="package" version="0.6.2">bwa</requirement> |
| 8 <requirement type="package" version="1.0.1">crest</requirement> | 8 <requirement type="package" version="1.0.1">crest</requirement> |
| 9 <requirement type="package" version="latest">blat_server</requirement> | 9 <requirement type="package" version="latest">blat_server</requirement> |
| 10 <requirement type="package" version="3">cap3</requirement> | 10 <requirement type="package" version="3">cap3</requirement> |
| 130 <help> | 130 <help> |
| 131 SHEAR-SV will process a BAM alignment file to find SVs and estimate the | 131 SHEAR-SV will process a BAM alignment file to find SVs and estimate the |
| 132 heterogeneity level of those SVs. It will output a *.report file reporing the | 132 heterogeneity level of those SVs. It will output a *.report file reporing the |
| 133 SVs and their heterogeneity levels, and it will output a *.sdi file that can be | 133 SVs and their heterogeneity levels, and it will output a *.sdi file that can be |
| 134 used for SHEAR-Assemble to reconstruct the new genome. | 134 used for SHEAR-Assemble to reconstruct the new genome. |
| 135 | |
| 136 Please cite the following article: | |
| 137 | |
| 138 Landman SR, Hwang TH, Silverstein KAT, Li Y, Dehm SM, Steinbach M, and Kumar V. SHEAR: sample heterogeneity estimation and assembly by reference. BMC Genomics 2014, 15:84. | |
| 139 | |
| 135 </help> | 140 </help> |
| 136 </tool> | 141 </tool> |