BOL

github.com - ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to...

github.com - Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding...

github.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...

atifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...

converting a VCF file into a FASTA file given a reference sequence

sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...

github.com - SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity,...

cab.spbu.ru - QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST  package starting from version 5.0.0 (download the latest release). Run QUAST as...

To decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655

github.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...