BOL

Comparative genomics educational material and papers bookmarks https://github.com/iansealy/coursera-comparinggenomes

ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...

Store all files in a array using perl: my @filesbwa = <$base_name/reads/$base_name.$library.bwa.*fa> #Store #Keep #Array #Perl

I recently used ABySS new program "abyss-mergepairs", source code https://github.com/bcgsc/abyss/blob/master/Align/mergepairs.cc You can also try USEARCH https://academic.oup.com/bioinformatics/article/31/21/3476/194979 Hope useful.

I want to merge PE reads. Can you please suggest me good tools.

#Error filtering, pair assembly and error #correction for next-generation sequencing #reads https://academic.oup.com/bioinformatics/article/31/21/3476/194979

Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...

Common usage  SPAdes: de Bruijn graph based assembler The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final assembly from multiple kmers. A list of kmers is...

Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a...

Remove the unwanted characters from Fasta file: sed -e '/^[^>]/s/[^ATGCatgc]/N/g' infile.fa #sed #unwanted #illegal #remove #correct #fasta #linux

Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs...

Bioinformatics JRF at IIT https://www.iitr.ac.in/administration/uploads/File/bt/2017/adv30112017.pdf #JRF

PeerJ also accept bioinformatics papers https://peerj.com