forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
README
28 lines (18 loc) · 1 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
See INSTALL for building and installation instructions.
Using an optimised zlib library
===============================
Samtools has been minimally tested against both the Intel-optimised and
CloudFlare-optimised zlibs and shown to work.
They can be downloaded from:
https://github.com/jtkukunas/zlib # Intel
https://github.com/cloudflare/zlib # CloudFlare
Neither Samtools nor HTSlib needs recompiling to use these optimised libraries,
but the LD_LIBRARY_PATH environment variable should be set to a directory
containing the libz.so.1 file.
Benchmarks comparing the various zlibs are available at:
http://www.htslib.org/benchmarks/zlib.html
It is recommended that you perform your own rigorous tests for an entire
pipeline if you wish to switch to one of the optimised zlib implementations.