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--- cluster:73 [2021/08/25 12:49]
hmeij07 [Rstudio]
+++ cluster:73 [2021/08/30 17:46]
hmeij07 [Paleogenomics Tools]
@@ Line 641: / Line 641: @@
 </code>
-  * https://github.com/ncbi/sra-tools/
+  * **sratools** https://github.com/ncbi/sra-tools/
   * The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
   * requires centos7 (glibc) so queues mwgpu, amber128, exx96
@@ Line 650: / Line 650: @@
 </code>
+  * **adapterremoval** https://adapterremoval.readthedocs.io/en/latest/index.html
+  * **bwa** https://github.com/lh3/bwa
+  * **bowtie2** http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+These are all part of Miniconda3, to setup the environment consult
+<code>
+[hmeij@greentail52 ~]$ conda list | egrep "adapterremoval|bwa|bowtie"
+adapterremoval            2.3.2                hb7ba0dd_0    bioconda
+bowtie2                   2.2.5            py38hed8969a_7    bioconda
+bwa                       0.7.17               hed695b0_7    bioconda
+</code>

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