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
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
Source: ea-utils
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
libbam-dev,
zlib1g-dev,
libgsl-dev,
libsparsehash-dev (>= 2.0)
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ea-utils.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/ea-utils.git
Homepage: https://expressionanalysis.github.io/ea-utils/
Package: ea-utils
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
r-base-core,
r-cran-getopt,
r-cran-hmisc,
r-cran-lattice,
r-cran-survival,
r-cran-formula,
r-cran-ggplot2
Recommends: med-config (>= 2.1)
Description: command-line tools for processing biological sequencing data
Ea-utils provides a set of command-line tools for processing biological
sequencing data, barcode demultiplexing, adapter trimming, etc.
.
Primarily written to support an Illumina based pipeline - but should work with
any FASTQs.
.
Main Tools are:
.
* fastq-mcf
Scans a sequence file for adapters, and, based on a log-scaled threshold,
determines a set of clipping parameters and performs clipping. Also does
skewing detection and quality filtering.
* fastq-multx
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
master set fields. Keeps multiple reads in-sync during demultiplexing. Can
verify that the reads are in-sync as well, and fail if they're not.
* fastq-join
Similar to audy's stitch program, but in C, more efficient and supports some
automatic benchmarking and tuning. It uses the same "squared distance for
anchored alignment" as other tools.
* varcall
Takes a pileup and calculates variants in a more easily parameterized manner
than some other tools.
|
