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Peregrine & SHIMMER Genome Assembly Toolkit
By Abhi 1640 days agogithub.com - Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...CLAW: Chloroplast Long-read Assembly Workflow
By LEGE 843 days agogithub.com - CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore...LRCstats: Long Read Correction Statistics
By Jit 3081 days agogithub.com - 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...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 3134 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...Fix rewritable error of ELGG !
By Abhi 1671 days ago Comments (1)www.digitalocean.com - The mod_rewrite module uses a rule-based rewriting engine, based on a PCRE regular-expression parser, to rewrite requested URLs on the fly. By default, mod_rewrite maps a URL to a filesystem path. However, it can also be used to...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1988 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...ARCS: scaffolding genome drafts with linked reads
By Rahul Nayak 3021 days agogithub.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...
Frequent Paired-end reads (PE 2x100) mapping command lines
Last updated 2951 days ago by Jitbowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam bwa bwasw...minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
By Jit 2942 days agogithub.com - Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining,...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2923 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...
