🌺 reference-free transcriptome assembly for short and long reads

A battery of methylation tools for PacBio HiFi reads

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

Detect and phase minor SNVs from long-read sequencing data

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.…

Re-implementation of J. Beaulaurier et al's SMSN strategy, using the default PacBio tools

a complete workflow that can be dockerized for the long read assembly, it allows for the genome assembly update as well as it allows for the assembly from the start. if you have the illumina reads it allows for the genome mapping also

De novo repeat inference from long reads

Patch for LRSDAY v1.6 for Debian-based and SUSE-based OS.

Identify and characterize repeat expansions in long read data

a long read repeat coverage calculator,given an long read file before assembly either direct from the sequencing runs or after the cleaning, it calculates the total amount of the repeat stretches present in the sequencing reads and you can plot them before assembly

Snakemake workflow for SM-PATseq

a shell code getter for genomics alignments for the illumina and long reads from pacbio and the oxfordnanopore

a slurm configuration analytical pipline for the analysis of the pacbiohifi sequencing genomes using the verkko, hifiasm and the genomeasm4pg. only provide the link to the sequencing or the files with the folder and rest it will do the work

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

awk simulators for the pacbiohifi assembly reading from the graphs. easy to use awk for the coverage and the length files. udpating later on with the complete awk functionalities for the compilation into the direct kernels.

genome sorting and plotting the length alignment from the lastz alignment for the node calculations right before you import them for the calculations.

A implication of stringr package to calculate the pattern detection in R using the stringR package for the pacbio and the oxford nanopore reads

a conda yaml for the genomehifi-contiguity that will allow you to create the environment for all the analysis.

a pacbiohifi read check for the quick view of the read types.