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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (203 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (659 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (820 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (873 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Carefully opt for human reference genome
By biogeek 1775 days agolh3.github.io - Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome. if you map reads to GRCh38 or hg38, use the...pbmm2:A minimap2 frontend for PacBio native data formats
By BioStar 1775 days agogithub.com - 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...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1776 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...SeqMule: Automated human exome/genome variants detection
By BioStar 1776 days agodoc-openbio.readthedocs.io - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of...
By Jit 1776 days agocatchenlab.life.illinois.edu - Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to...Machine learning in Perl
By Jit 1777 days agoblogs.perl.org - this is a fourth blog post in the Machine learning in Perl series, focusing on the AI::MXNet, a Perl interface to Apache MXNet, a modern and powerful machine learning library. If you're interested in refreshing your memory or just new to the...iSeqQC: a tool for expression-based quality control in RNA sequencing
By BioStar 1777 days agogithub.com - 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,...CLARK: Fast, accurate and versatile sequence classification system
By Jit 1779 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 1779 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:Cancer Dependency Map
By Jit 1780 days agodepmap.sanger.ac.uk - The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This...
