Differences

This shows you the differences between two versions of the page.

--- cluster:73 [2020/01/14 14:29]
hmeij07 [Paleogenomics Tools]
+++ cluster:73 [2020/01/14 15:07]
hmeij07 [Paleogenomics Tools]
@@ Line 16: / Line 16: @@
 Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
+  * http://www.htslib.org/download/
   * Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
   * BCFtools:Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
@@ Line 22: / Line 23: @@
 <code>
- export PATH=/share/apps/CENTOS6/samtools/1.10/bin:$PATH
+# add to environment
+export PATH=/share/apps/CENTOS6/samtools/1.10/bin:$PATH
+export PATH=/share/apps/CENTOS6/bcftools/1.10.2/bin:$PATH
+export PATH=/share/apps/CENTOS6/htslib/1.10.2/bin:$PATH
 </code>
+   * https://github.com/ANGSD/angsd
+   * Program for analysing NGS data
+<code>
+# does not seem to work against htslib version above...
+export  HTSSRC=/share/apps/CENTOS6/ANGSD/htslib
+export PATH=/share/apps/CENTOS6/ANGSD/angsd:$PATH
+</code>
+  * https://www.beast2.org/
+  * BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
+<code>
+# with local java jre1.8.0_212
+export PATH=/share/apps/CENTOS6/beast/2.6.0/bin:$PATH
+</code>
 ====== CD-HIT ======

DokuWiki