PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), an...nd clonality. PureCN is designed for targeted short read sequencing data, integrates w...calling and SNV classification using targeted short read seque...2153 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-...as an implicit de Bruijn graph. Each long read is then corrected independently by...2152 days ago
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, together...2152 days ago
2148 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or th...ade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly,...s and the more erroneous long reads are corrected using the shor...t machine learning-based long read error correction algorithm. The algorithm mode...2142 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...nd eukaryotic. However, short reads are difficult to assemble and...age the high quality of short reads to correct errors in long re...nmapped mates of mapped short reads. Our results on bacterial, f...res well with existing hybrid correction methods.The source code of Co...2142 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 the...ic Biosciences SMRT error model. Reads are simulated from both stra...quence. The reference can be read from a FASTA file or randomly...orporated at a later stage.) The read lengt...2140 days ago
LRCstats: a tool for evaluating long reads correction methods
LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generatio...ed by Illumina. However, long reads are plagued by high error rates, w...ownstream analysis. Long read correction algorithms reduce the error r...2140 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...we use an iterative alignment-free correction method based on de Brui...;k-mers, and second, the corrected reads are further p...most accurate one relying on long reads only for read sets with high cover...2125 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 by --long_read_batch...2125 days ago