Results for "Long"
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SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA m...Tags: SALSA, tool, scaffold, long, read, assemblies, Hi-C, Genome
2142 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect...Tags: ReMILO, reference, assisted, misassembly, detection, algorithm, short, long, reads
2121 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofiltTags: nanofilt, filter, trim, long, read, sequencing, NGS, nanopore
2096 days ago
LSC :a long read error correction tool
Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how LSC works on some example data. Read the ...Tags: LSC, long, read, error, correction, tool, fast, correction, sensitivity, good, accuracy
2094 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the pa...Tags: LR_Gapcloser, tiling, path-based, gap, closer, long, reads, complete, genome, assembly
1442 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 destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python finisherSC.py -par 20 destinedFolder mummerPath S...Tags: FinisherSC, repeat-aware, tool, upgrading, de novo, assembly, long, reads
2076 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 accurate reads including de novo assembly, fusion and structural variation detection. In such cases researchers often combine both tech...Tags: Hercules, profile, HMM-based, hybrid, error, correction, algorithm, long, reads, PacBio
2075 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 generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are lon...Tags: LRCstats, tool, evaluation, long, reads, correction, methods
2073 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: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependenci...Tags: LoRMA, tool, correction, sequencing, errors, long, reads, PacBio, SMRT
2058 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 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the task of testing basecallers). It should in pri...Tags: Rebaler, program, conducting, reference-based, assemblies, long, reads, ont, pacbio
2047 days ago
