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abdenlab
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oxbow
Read specialized NGS formats as data frames in R, Python, and more.
https://lifeinbytes.substack.com/p/breaking-out-of-bioinformatic-data-silos
Apache License 2.0
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Range query API
#55
Open
GarrettNg
opened
11 months ago
GarrettNg
commented
11 months ago
Partially implemented (some may already be implemented)
[ ] alignments:
[ ] sam.gz:
[ ] tbi
[ ] csi
[ ] bam: bai/csi
[x] bai
[ ] tbi
[ ] csi
[ ] cram
[ ] tbi
[x] csi
[ ] variants:
[ ] vcf
[x] tbi
[ ] csi
[ ] bcf
[ ] tbi
[x] csi
[ ] sequences: fasta, fastq
[ ] fasta.gz
[x] fai (fasta, uncompressed)
[] gzi (compressed)
[ ] fastq.gz
[x] fai (fastq, uncompressed)
[ ] gzi (compressed)
[ ] interval feature
[ ] bed.gz
[ ] bedGraph.gz
[ ] gtf.gz/gff.gz
[ ] Arbitrary TSV files with tabix
Partially implemented (some may already be implemented)