Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update README #15

Merged
merged 1 commit into from
Sep 13, 2023
+41 −6
Merged

Update README #15

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 17 additions & 6 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,12 +1,23 @@
# STELLAR3 - the SwifT Exact LocaL AligneR
This is similar to [STELLAR](https://github.com/seqan/seqan/tree/master/apps/stellar) but adapted for seqan3 usage and
added new cool features.
This is similar to [STELLAR](https://github.com/seqan/seqan/tree/master/apps/stellar) but uses the [sharg parser](https://docs.seqan.de/seqan3/3-master-user/tutorial_argument_parser.html) and can be used to narrow the search to only a segment of the reference database.


Instructions:
## Building Stellar3:
1. clone this repository: `git clone --recurse-submodules https://github.com/seqan/stellar3`
2. create a build directory and visit it: `mkdir stellar3/build && cd $_`
3. run cmake: `cmake ..`
4. build the application: `make`
5. optional: build and run the tests: `make test`
6. execute the app: `./bin/stellar --help`
5. show the help page: `./bin/stellar --help`

## Running Stellar3:
The `example` folder contains example data for a test run. Stellar3 can be used to produce soft-clipped read alignments or to find all local alignments between two genomes.

Searching the reference sequences for local alignments with a minimum length of 50 and a maximum error rate of 0.02:
`./bin/stellar -e 0.02 -l 50 -o mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`

Searching only a segment of the reference for local alignments:
`./bin/stellar --sequenceOfInterest 0 --segmentBegin 5000 --segmentEnd 7500 -e 0.02 -l 50 -o segment.mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`

Finding all local alignments between two related genomes:
`./bin/stellar -e 0.1 -l 50 -o alignments.gff ../example/NC_001474.fasta ../example/NC_001477.fasta`

See the original [documentation](https://github.com/seqan/seqan/tree/main/apps/stellar) for details on the Stellar output formats.
0 src/example/NC_001474.fasta → example/NC_001474.fasta
View file
Open in desktop
File renamed without changes.
0 src/example/NC_001477.fasta → example/NC_001477.fasta
View file
Open in desktop
File renamed without changes.
14 changes: 14 additions & 0 deletions example/alignments.gff
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
gi|158976983|ref|NC_001474.2| Stellar eps-matches 10542 10723 90.3225 + . gi|9626685|ref|NC_001477.1|;seq2Range=10553,10735;eValue=2.35373e-61;cigar=30M1D5M1I22M1D7M1I1M1I50M1D2M1I62M;mutations=10C,11A,13C,16G,17G,27C,28C,32G,36T,66C,68C,74C,97G,121A,149A
gi|158976983|ref|NC_001474.2| Stellar eps-matches 10558 10723 91.7647 + . gi|9626685|ref|NC_001477.1|;seq2Range=10570,10735;eValue=2.74788e-59;cigar=1D15M1D3M1I28M1I1M1D1M1I50M1D2M1I62M;mutations=10C,11C,14G,19T,48G,51C,57C,80G,104A,132A
gi|158976983|ref|NC_001474.2| Stellar eps-matches 9601 9710 90.09 + . gi|9626685|ref|NC_001477.1|;seq2Range=9602,9711;eValue=1.90335e-33;cigar=78M1D1M1I30M;mutations=10T,12G,28G,30A,33A,44C,45G,62A,80A,90T
gi|158976983|ref|NC_001474.2| Stellar eps-matches 10290 10384 90.625 + . gi|9626685|ref|NC_001477.1|;seq2Range=10311,10405;eValue=8.52734e-29;cigar=79M1D4M1I11M;mutations=10A,21C,37C,42T,45G,47G,55G,84T
gi|158976983|ref|NC_001474.2| Stellar eps-matches 10441 10520 90 + . gi|9626685|ref|NC_001477.1|;seq2Range=10456,10534;eValue=4.46015e-22;cigar=9M1D70M;mutations=9C,19T,20G,46G,51C,52A,59T
gi|158976983|ref|NC_001474.2| Stellar eps-matches 43 121 90 + . gi|9626685|ref|NC_001477.1|;seq2Range=42,118;eValue=4.46015e-22;cigar=3M1I4M1D26M1D43M1D;mutations=4A,8T,12T,59C,75A
gi|158976983|ref|NC_001474.2| Stellar eps-matches 3093 3157 90.7692 + . gi|9626685|ref|NC_001477.1|;seq2Range=3091,3155;eValue=1.99822e-17;cigar=65M;mutations=13C,19T,22A,37C,40G,58C
gi|158976983|ref|NC_001474.2| Stellar eps-matches 5419 5477 90 + . gi|9626685|ref|NC_001477.1|;seq2Range=5420,5478;eValue=7.66823e-15;cigar=16M1D1M1I41M;mutations=9C,18T,27A,35C,42C
gi|158976983|ref|NC_001474.2| Stellar eps-matches 9046 9101 91.0714 + . gi|9626685|ref|NC_001477.1|;seq2Range=9047,9102;eValue=2.52061e-14;cigar=56M;mutations=19A,20G,30T,33A,36C
gi|158976983|ref|NC_001474.2| Stellar eps-matches 3400 3452 90.566 + . gi|9626685|ref|NC_001477.1|;seq2Range=3398,3450;eValue=8.95234e-13;cigar=53M;mutations=3C,18C,34G,36C,45G
gi|158976983|ref|NC_001474.2| Stellar eps-matches 7785 7835 90.3846 + . gi|9626685|ref|NC_001477.1|;seq2Range=7789,7839;eValue=2.94271e-12;cigar=15M1I1M1D34M;mutations=16C,19A,34A,40T
gi|158976983|ref|NC_001474.2| Stellar eps-matches 131 180 90.196 + . gi|9626685|ref|NC_001477.1|;seq2Range=129,178;eValue=9.67292e-12;cigar=42M1I3M1D4M;mutations=22C,38A,43T,45T
gi|158976983|ref|NC_001474.2| Stellar eps-matches 7066 7115 90 + . gi|9626685|ref|NC_001477.1|;seq2Range=7070,7118;eValue=3.17957e-11;cigar=45M1D4M;mutations=10A,12A,27A,36A
gi|158976983|ref|NC_001474.2| Stellar eps-matches 8989 9038 90.196 + . gi|9626685|ref|NC_001477.1|;seq2Range=8990,9039;eValue=9.67292e-12;cigar=15M1D2M1I32M;mutations=18G,24G,30T,48T
7 changes: 7 additions & 0 deletions example/mapped_reads.gff
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
gi|9626685|ref|NC_001477.1| Stellar eps-matches 10580 10629 98.0392 + . read01;seq2Range=24,74;eValue=4.77542e-20;cigar=19M1I31M;mutations=20C
gi|9626685|ref|NC_001477.1| Stellar eps-matches 6870 6923 98.1818 + . read03;seq2Range=46,100;eValue=4.09044e-22;cigar=29M1I25M;mutations=30C
gi|9626685|ref|NC_001477.1| Stellar eps-matches 6418 6519 98.0392 + . read04;seq2Range=1,100;eValue=7.44922e-45;cigar=76M1D24M1D;mutations=
gi|9626685|ref|NC_001477.1| Stellar eps-matches 9160 9222 98.4126 + . read08;seq2Range=11,73;eValue=3.00114e-26;cigar=63M;mutations=52N
gi|9626685|ref|NC_001477.1| Stellar eps-matches 7149 7217 98.5507 + . read10;seq2Range=1,69;eValue=2.37916e-29;cigar=69M;mutations=48A
gi|9626685|ref|NC_001477.1| Stellar eps-matches 9870 9939 98.5915 - . read02;seq2Range=1,71;eValue=2.20193e-30;cigar=20M1I50M;mutations=21C
gi|9626685|ref|NC_001477.1| Stellar eps-matches 9056 9151 98.9583 - . read06;seq2Range=6,100;eValue=2.64571e-43;cigar=2M1D93M;mutations=
0 src/example/reads.fasta → example/reads.fasta
View file
Open in desktop
File renamed without changes.
3 changes: 3 additions & 0 deletions example/segment.mapped.reads.gff
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
gi|9626685|ref|NC_001477.1| Stellar eps-matches 6870 6923 98.1818 + . read03;seq2Range=46,100;eValue=4.09044e-22;cigar=29M1I25M;mutations=30C
gi|9626685|ref|NC_001477.1| Stellar eps-matches 6418 6519 98.0392 + . read04;seq2Range=1,100;eValue=7.44922e-45;cigar=76M1D24M1D;mutations=
gi|9626685|ref|NC_001477.1| Stellar eps-matches 7149 7217 98.5507 + . read10;seq2Range=1,69;eValue=2.37916e-29;cigar=69M;mutations=48A