🌺 reference-free transcriptome assembly for short and long reads
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Updated
Jan 28, 2024 - Java
🌺 reference-free transcriptome assembly for short and long reads
A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.…
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Patch for LRSDAY v1.6 for Debian-based and SUSE-based OS.
Snakemake workflow for SM-PATseq
code getter for illumina, pacbio, oxford long reads alignments.
bcftools for dealing with bcf files.
A battery of methylation tools for PacBio HiFi reads
awk code for pacbiohifi alignments from verkko and other genome assembly methods
lastz alignment sorting and plotting the alignment length
Identify and characterize repeat expansions in long read data
pacbiohifi sequencing genomes analysis using the verkko, hifiasm and the genomeasm4pg.
genome assembly to pangraphs from illumina to long reads.
Detect and phase minor SNVs from long-read sequencing data
De novo repeat inference from long reads
pacbio or oxford nanopore long reads repeat coverage estimation.
Re-implementation of J. Beaulaurier et al's SMSN strategy, using the default PacBio tools
pattern detection in R using the stringR package for the pacbio and the oxford nanopore reads
a conda yaml for the genomehifi-contiguity analysis.
long_read_polyATGC_trimmer using regular expression.
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