sickle 1.33-1 source package in Ubuntu
Changelog
sickle (1.33-1) unstable; urgency=medium * Initial upload to Debian (Closes: #789707) -- Andreas Tille <email address hidden> Tue, 23 Jun 2015 21:08:09 +0200
Upload details
- Uploaded by:
- Debian Med
- Uploaded to:
- Sid
- Original maintainer:
- Debian Med
- Architectures:
- any
- Section:
- misc
- Urgency:
- Medium Urgency
See full publishing history Publishing
| Series | Published | Component | Section | |
|---|---|---|---|---|
| Xenial | release | universe | misc |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| sickle_1.33-1.dsc | 1.9 KiB | 55011005d688aea1c6c22740c1537d50f51c09b30696f4d130ddf17b9524361b |
| sickle_1.33.orig.tar.gz | 616.5 KiB | eab271d25dc799e2ce67c25626128f8f8ed65e3cd68e799479bba20964624734 |
| sickle_1.33-1.debian.tar.xz | 2.9 KiB | e19c8d62594766ffb007c6f82be7a18af362df24ea35a1872654fd08d74eea26 |
No changes file available.
Binary packages built by this source
- sickle: No summary available for sickle in ubuntu yakkety.
No description available for sickle in ubuntu yakkety.
- sickle-dbgsym: debug symbols for package sickle
Most modern sequencing technologies produce reads that have deteriorating
quality towards the 3'-end. Incorrectly called bases here negatively impact
assembles, mapping, and downstream bioinformatics analyses.
.
Sickle is a tool that uses sliding windows along with quality and length
thresholds to determine when quality is sufficiently low to trim the 3'-end
of reads. It will also discard reads based upon the length threshold. It takes
the quality values and slides a window across them whose length is 0.1 times
the length of the read. If this length is less than 1, then the window is set
to be equal to the length of the read. Otherwise, the window slides along the
quality values until the average quality in the window drops below the
threshold. At that point the algorithm determines where in the window the drop
occurs and cuts both the read and quality strings there. However, if the cut
point is less than the minimum length threshold, then the read is discarded
entirely.
.
Sickle supports four types of quality values: Illumina, Solexa, Phred, and
Sanger. Note that the Solexa quality setting is an approximation (the actual
conversion is a non-linear transformation). The end approximation is close.
.
Sickle also supports gzipped file inputs.
