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fulcrumgenomics
/
fqtk
Fast FASTQ sample demultiplexing in Rust.
MIT License
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chore: add tfenne and nh13 as codeowners
#49
nh13
closed
2 weeks ago
0
Fix early return and counting of mismatches with no-calls in barcodes.
#48
theJasonFan
closed
2 weeks ago
0
Demultiplexing "N"-barcode as no-op
#47
mschubert
closed
2 weeks ago
3
doc: improved explanation of metadata TSV formatting for multiple barcodes
#46
TimD1
opened
1 month ago
0
Improved `fqtk demux --help` output readability
#45
TimD1
opened
1 month ago
0
feat: better error message when barcode length differs from expected
#44
TimD1
opened
2 months ago
1
Adds test for better fgoxide header error and bump fgoxide version.
#43
theJasonFan
opened
4 months ago
0
doc: Clarify that multiple output types may be specified
#42
msto
closed
4 months ago
1
how to obtain demultixepled paired-end reads with same structure as input reads, including cell barcodes / UMIs
#41
andreiprodan
closed
4 months ago
2
Barcodes only in Read 1
#40
ahish-sujay
closed
4 months ago
6
Clippy the tests and make it happy.
#39
theJasonFan
closed
6 months ago
0
DRAFT: SortFastq
#38
kockan
opened
1 year ago
0
fq trimming
#37
brentp
opened
1 year ago
0
Request for example sample-metadata file
#36
JHarrisonEcoEvo
opened
1 year ago
2
Add demux to readme.
#35
tfenne
closed
1 year ago
0
fqtk demux's usage is full of MarkDown that comes out verbatim on the console
#34
tfenne
opened
1 year ago
0
[bugfix] Output type writers were all outputting template reads.
#33
jacarey
closed
1 year ago
0
feat: skip too short reads
#32
nh13
closed
1 year ago
0
Better error when the sample barcode lengths in the meta do not match the barcode lengths in the read structure
#31
nh13
opened
1 year ago
2
feat: allow Ns in the sample barcode
#30
nh13
closed
1 year ago
0
Support barcodes that have different lengths
#29
nh13
closed
2 months ago
1
Fails if sample barcodes in the meta.csv are longer than implied by the read structure
#28
nh13
closed
1 month ago
1
FQTK fails if reads are too short
#27
nh13
closed
1 year ago
0
Do not require comment to have 4 segments
#26
nh13
closed
1 year ago
0
"Comment in did not have 4 segments" in data from SRA/ENA
#25
nh13
closed
1 year ago
0
Fixing rust version in CI because TOML toolchain was not being honored previously.
#24
NatPRoach
closed
1 year ago
0
Tool-chain version of clippy not being honored
#23
NatPRoach
opened
1 year ago
2
Add 'version' arg to command line derivations
#22
NatPRoach
closed
1 year ago
3
Check skipped sequence?
#21
mschubert
closed
1 year ago
5
Reserve capacity to avoid multiple re-allocations
#20
tfenne
closed
1 year ago
0
Integrate read ahead iterator from fgoxide.
#19
NatPRoach
closed
1 year ago
1
Adding bioconda and crates badges, updating install instructions
#18
NatPRoach
closed
1 year ago
0
Removing publish=false from TOML to prepare for impending crates / bioconda release
#17
NatPRoach
closed
1 year ago
0
Add docs for releasing
#16
nh13
closed
1 year ago
0
Merge dev into main.
#15
tfenne
closed
1 year ago
0
Lots of performance tuning, and then adding adding sequences into read headers.
#14
tfenne
closed
1 year ago
0
Adding initial metrics generation.
#13
NatPRoach
closed
1 year ago
0
Adding preallocation vector for ref records
#12
NatPRoach
closed
1 year ago
1
Task 8 - Adding the sample barcodes and molecular barcodes to headers.
#11
NatPRoach
closed
1 year ago
0
Various performance improvements including iterating over ref records, and using mono-pooled writer
#10
NatPRoach
closed
1 year ago
2
bugfix - fixing layered buf reader issue with seq_io
#9
NatPRoach
closed
1 year ago
1
Adding rudimentary caching of barcodes
#8
NatPRoach
closed
1 year ago
0
Adding support for a pooled writer to working core
#7
NatPRoach
closed
1 year ago
0
Implement working core of demux FASTQs without caching and without pooled writing
#6
NatPRoach
closed
1 year ago
0
Implement basic command line for fqtk demux
#5
NatPRoach
closed
1 year ago
0
Task3/sample metadata
#4
NatPRoach
closed
1 year ago
0
New tool: replicate fgbio's SortFastq?
#3
tfenne
opened
1 year ago
0
Task2/basic barcode matching struct
#2
NatPRoach
closed
1 year ago
0
Task1/initial repo setup
#1
NatPRoach
closed
1 year ago
0