<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37643?offset=80 https://bioinformaticsonline.com/bookmarks/view/36533/mecat-fast-mapping-error-correction-and-de-novo-assembly-for-single-molecule-sequencing-reads Fri, 11 May 2018 05:07:45 -0500 https://bioinformaticsonline.com/bookmarks/view/36533/mecat-fast-mapping-error-correction-and-de-novo-assembly-for-single-molecule-sequencing-reads <![CDATA[MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads]]> MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faster than the current PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON. 

https://www.nature.com/articles/nmeth.4432

Address of the bookmark: https://github.com/xiaochuanle/MECAT

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads Mon, 11 Jun 2018 05:14:57 -0500 https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads <![CDATA[npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads]]> Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Sat, 06 Jul 2019 03:48:22 -0500 https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing Sun, 16 Feb 2020 08:47:17 -0600 https://bioinformaticsonline.com/bookmarks/view/41046/iseqqc-a-tool-for-expression-based-quality-control-in-rna-sequencing <![CDATA[iSeqQC: a tool for expression-based quality control in RNA sequencing]]> iSeqQC, an expression-based QC tool that detects outliers either produced due to variable laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers.

http://cancerwebpa.jefferson.edu/iSeqQC/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3399-8

Address of the bookmark: https://github.com/gkumar09/iSeqQC

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40897/mec-contig-misassembly-correction Tue, 04 Feb 2020 23:40:49 -0600 https://bioinformaticsonline.com/bookmarks/view/40897/mec-contig-misassembly-correction <![CDATA[MEC: Contig Misassembly Correction]]> MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the statistical analysis of GC-contents. We apply MEC to four real contig datasets, and carry out experiments to analyze the influence of MEC on scaffolding results, which shows that MEC can reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available for download at https://github.com/bioinfomaticsCSU/MEC.

Address of the bookmark: https://github.com/bioinfomaticsCSU/MEC

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/38012/cosine-non-seeding-method-for-mapping-long-noisy-sequences Fri, 26 Oct 2018 00:41:59 -0500 https://bioinformaticsonline.com/bookmarks/view/38012/cosine-non-seeding-method-for-mapping-long-noisy-sequences <![CDATA[COSINE: non-seeding method for mapping long noisy sequences]]> Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.

Address of the bookmark: https://github.com/SUwonglab/COSINE

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32905/bigmac-breaking-inaccurate-genomes-and-merging-assembled-contigs-for-long-read-metagenomic-assembly Mon, 22 May 2017 05:43:51 -0500 https://bioinformaticsonline.com/bookmarks/view/32905/bigmac-breaking-inaccurate-genomes-and-merging-assembled-contigs-for-long-read-metagenomic-assembly <![CDATA[BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly]]> This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit Lam.

https://github.com/kakitone/MetaFinisherSC

https://github.com/kakitone/BIGMAC

Address of the bookmark: https://github.com/kakitone/BIGMAC

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32943/npscarf-scaffolding-and-completing-assemblies-in-real-time-fashion Tue, 23 May 2017 04:53:29 -0500 https://bioinformaticsonline.com/bookmarks/view/32943/npscarf-scaffolding-and-completing-assemblies-in-real-time-fashion <![CDATA[npScarf: Scaffolding and Completing Assemblies in Real-time Fashion]]> npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of positional information such as gene ordering and the detection of genes from mobile elements (plasmids and genomic islands).

Complete paper at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321748/

Address of the bookmark: https://github.com/mdcao/npScarf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats Tue, 18 Feb 2020 03:36:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats <![CDATA[pbmm2:A minimap2 frontend for PacBio native data formats]]> pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

Address of the bookmark: https://github.com/PacificBiosciences/pbmm2

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 Mon, 10 Apr 2017 04:45:40 -0500 https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 <![CDATA[WGS Celera Assembler version 8.3rc2]]> These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.

This distribution package provides a stable, tested, documented version of the software.  The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.

The source code package includes full source code (revision 4627), Makefiles, and scripts.  A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included.  This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].

Full documentation can be found online at http://wgs-assembler.sourceforge.net/.

Interesting scripts within it

urbe@urbo214b[bin] ls                                                        []
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-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw
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-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze
-rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample
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-rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap
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-rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique
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-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore
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lrwxrwxrwx 1 urbe urbe    4 Apr 10 11:41 pacBioToCA -> PBcR
-rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR
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-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap
-rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq
-rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap
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-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache
-rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA
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-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA
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-rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore
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-rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracedb-to-frg.pl
-rwxrwxr-x 1 urbe urbe  44K Apr 10 11:41 trimFastqByQVWindow
-rwxrwxr-x 1 urbe urbe  18K Apr 10 11:40 uidclient
-rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger
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-rwxrwxr-x 1 urbe urbe  854 Apr 10 11:41 utg2fasta
-rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns
-rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix


Address of the bookmark: http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page

]]> Jit