FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python fin...computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python fi...e a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads...2137 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third gen...ral studies require long and accurate reads including de novo assembly, f...hnologies and the more erroneous long reads are corrected using the short...uses this to correct errors in these reads. Using datasets from two DNA-...2137 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing techno...nd eukaryotic. However, short reads are difficult to assemble and...e recent developments in long reads sequencing methods offer a pr...age the high quality of short reads to correct errors in long rea...nmapped mates of mapped short reads. Our results on bacterial, fu...2137 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on th...Biosciences SMRT error model. Reads are simulated from both stran...ture is respected when drawing reads. (Simulation of genome rearra...g to number of passes Outputs reads in FASTQ format and alignment...2135 days ago
LRCstats: a tool for evaluating long reads correction methods
LRCstats is an open-source pipeline for ben...g read correction algorithms for long reads outputted by third generation...produced by Pacific Biosciences. The reads produced by third generation...e produced by Illumina. However, long reads are plagued by high error rat...2135 days ago
LoRMA: A tool for correcting sequencing errors in long reads
An error correction method that uses long reads only. The method consists of two phases: fir...th of k-mers, and second, the corrected reads are further polished using lo...hod is the most accurate one relying on long reads only for read sets with high...2120 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set...2120 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genom...for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our m...2119 days ago
Rebaler: program for conducting reference-based assemblies using long reads.
Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2&...2108 days ago
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