<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/33976?offset=650 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/40544/ngs-bits-short-read-sequencing-tools Thu, 16 Jan 2020 23:14:00 -0600 https://bioinformaticsonline.com/bookmarks/view/40544/ngs-bits-short-read-sequencing-tools <![CDATA[ngs-bits - Short-read sequencing tools]]> Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Address of the bookmark: https://github.com/imgag/ngs-bits

]]> Neel 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/42826/ktrim-an-extra-fast-and-accurate-adapter-and-quality-trimmer-for-sequencing-data Thu, 11 Feb 2021 21:39:05 -0600 https://bioinformaticsonline.com/bookmarks/view/42826/ktrim-an-extra-fast-and-accurate-adapter-and-quality-trimmer-for-sequencing-data <![CDATA[Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data]]> Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

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