[#UGENE-3324] Sanger reads quality control and alignment

[UGENE-3324] Sanger reads quality control and alignment Created: 30/Jul/14 Updated: 28/Apr/20 Resolved: 13/Feb/18
Status:	Closed
Project:	UGENE
Component/s:	Basic-MSA, Basic-Nucl
Affects Version/s:	None
Fix Version/s:	None

Type:

Epic

Priority:

Major

Reporter:

Olga Golosova

Assignee:

Unassigned

Resolution:

Fixed

Labels:

request, sanger, usability

Remaining Estimate:

Not Specified

Time Spent:

Not Specified

Original Estimate:

Not Specified

Issue Links:

Relates
relates to	~~UGENE-5582~~	The second stage of the Sanger Reads ...	Closed
relates to	~~UGENE-3251~~	Chromatograms longer than sequences	Closed
relates to	~~UGENE-3954~~	New WD element: align Sanger reads to...	Closed
relates to	~~UGENE-3958~~	Add WD sample for Sanger reads analysis	Closed

Epic Name:

Sanger

Sprint:

DEV-29/01/2015, DEV-12/02/2015

Affect Type:

Userdefined

Description

Think on how to improve the following procedure:

A region is sequenced with Sanger. There are several ABI files for it. The reads are shifted and some of them are reversed.
The quality of ends of the regions is poor, so the ends of the reads must be trimmed.
Then the reads must be aligned. The direction of the reads must be taken into account.

Comments

Comment by Olga Golosova [ 24/Feb/15 ]

One more request about aligning/editing chromotograms:
"I have recently downloaded your software for the purpose of editing and assembling sequences around 600-1000bp long. The software I am used to or this is sequencher and I was wondering if your software had the tools to enable me to edit both forward and reverse sequences (which have been assembled) by observing the chromatograms of each sequence?"

Comment by Olga Golosova [ 25/Feb/15 ]

One more request. Vector NTI is currently used by the user.
"It is handy to see the alignment and forward/reverse chromatograms at the same time..."

Comment by Olga Golosova [ 25/Feb/15 ]

A reference to one more request (the old one): http://ugene.unipro.ru/forum/YaBB.pl?num=1416477334/0

Comment by Olga Golosova [ 28/Feb/15 ]

A comment from ~~UGENE-1352~~ which is a duplicate of this issue:
"See Sequencher(http://genecodes.com/) or SnapGene for more detail.
The request is described in this discussion: http://vk.com/uniprougene?w=wall-74359225_134"

Comment by Olga Golosova [ 03/Mar/15 ]

See comment by a user: https://www.facebook.com/groups/ugene/permalink/1563852140550694/.

I want to to view the possible amino acid sequence in a nucleotide multiple seq alignment. For example in Mesquite you can view the nucleotide alignment and at the top you can view the amino acid seq base on each codon.

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[UGENE-3324] Sanger reads quality control and alignment Created: 30/Jul/14 Updated: 28/Apr/20 Resolved: 13/Feb/18