NanoPack: visualizing and processing long-read sequencing data
The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, togeth...2149 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py des...r raw_reads.fasta using the following command. perl -pe 's/>[^\$]*$/">Seg"...sta cp newRaw_reads.fasta raw_reads.fasta perl -pe 's/>[^\$]*$/">Seg"...2140 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accur...2139 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short...2139 days ago
Snakemake—a scalable bioinformatics workflow engine
Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.2126 days ago
2123 days ago
GenomeThreader: Gene Prediction Software
GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where add...2095 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads...2079 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodolo...2074 days ago
RopeBWT2: Incremental construction of FM-index for DNA sequences
RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pse...2074 days ago