readfq
minimap2
| readfq | minimap2 | |
|---|---|---|
| 2 | 5 | |
| 164 | 1,696 | |
| - | - | |
| 0.0 | 7.6 | |
| almost 3 years ago | 8 days ago | |
| C | C | |
| - | GNU General Public License v3.0 or later |
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readfq
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Training resources for Biopython?
Heng Li has a FASTQ/FASTA reader that I generally cut and paste into my code rather than use Biopython. Biopython has a very rich model for sequence data but you generally don't need 90% of it and it comes at a significant performance cost.
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Extract sequences given FASTA + list of starts and ends?
Just slap Heng Li's FASTQ/A parsing function in, load in your read, then loop through your coordinates and slice the sequence.
minimap2
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Ask HN: Comment here about whatever you're passionate about at the moment
Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.
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BLAST 10,000 genes?
No experience with this maybe try minimap2(https://github.com/lh3/minimap2) if this doesn't work fall back on blast/blat
- Truncating genome fastas to just overlapping regions
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Alignment of long reads to plasmid and generation of consensus sequence.
You can try minimap2 to align your long reads to your expected plasmid
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Questions about WGS mapping
It sounds like the mapping wasn't very good, you might want to try minimap2 as it is a newer algorithm.
What are some alternatives?
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
bwa-mem2 - The next version of bwa-mem
biofast - Benchmarking programming languages/implementations for common tasks in Bioinformatics
seqtk - Toolkit for processing sequences in FASTA/Q formats
bioawk - BWK awk modified for biological data
seqstats - Quick summary statistics on fasta/fastq(.gz) files
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
slivar - genetic variant expressions, annotation, and filtering for great good.
biomisc - collection of miscellaneous command line bioinformatic scripts
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
bwa-mem2 - The next version of bwa-mem
Klib - A standalone and lightweight C library