We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator design that adopts modern FPGA (field-programmable gate array) architectures to further boost the performance of our algorithm.

More at https://github.com/CMU-SAFARI/Shouji

Address of the bookmark: https://github.com/CMU-SAFARI/Shouji

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

Address of the bookmark: https://github.com/soedinglab/MMseqs2

Address of the bookmark: https://www.science.org/doi/10.1126/science.abj6987

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

Main features:

1. works with any number of scaffold assemblies in de-novo non-progressive fashion
2. allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
3. creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
4. constructs a merged combined scaffold assembly
5. provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

1. Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
   • selecting the type of identifier and pasting identifiers (one per line)
   • or by using the gene ID search tool
   • or with the BLAST search tool
2. Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

Address of the bookmark: https://github.com/sbg/geck

• File System
  ls — list items in current directory
  ls -l — list items in current directory and show in long format to see perimissions, size, and modification date
  ls -a — list all items in current directory, including hidden files
  ls -F — list all items in current directory and show directories with a slash and executables with a star
  ls dir — list all items in directory dir
  cd dir — change directory to dir
  cd .. — go up one directory
  cd / — go to the root directory
  cd ~ — go to to your home directory
  cd - — go to the last directory you were just in
  pwd — show present working directory
  mkdir dir — make directory dir
  rm file — remove file
  rm -r dir — remove directory dir recursively
  cp file1 file2 — copy file1 to file2
  cp -r dir1 dir2 — copy directory dir1 to dir2 recursively
  mv file1 file2 — move (rename) file1 to file2
  ln -s file link — create symbolic link to file
  touch file — create or update file
  cat file — output the contents of file
  less file — view file with page navigation
  head file — output the first 10 lines of file
  tail file — output the last 10 lines of file
  tail -f file — output the contents of file as it grows, starting with the last 10 lines
  vim file — edit file
  alias name 'command' — create an alias for a command
  
• System
  shutdown — shut down machine
  reboot — restart machine
  date — show the current date and time
  whoami — who you are logged in as
  finger user — display information about user
  man command — show the manual for command
  df — show disk usage
  du — show directory space usage
  free — show memory and swap usage
  whereis app — show possible locations of app
  which app — show which app will be run by default
  
• Process Management
  ps — display your currently active processes
  top — display all running processes
  kill pid — kill process id pid
  kill -9 pid — force kill process id pid
  
• Permissions
  ls -l — list items in current directory and show permissions
  chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.
  7 — full permissions
  6 — read and write only
  5 — read and execute only
  4 — read only
  3 — write and execute only
  2 — write only
  1 — execute only
  0 — no permissions
  chmod 600 file — you can read and write - good for files
  chmod 700 file — you can read, write, and execute - good for scripts
  chmod 644 file — you can read and write, and everyone else can only read - good for web pages
  chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
  
• Networking
  wget file — download a file
  curl file — download a file
  scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine
  scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server
  scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine
  ssh user@host — connect to host as user
  ssh -p port user@host — connect to host on port as user
  ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login
  ping host — ping host and output results
  whois domain — get information for domain
  dig domain — get DNS information for domain
  dig -x host — reverse lookup host
  lsof -i tcp:1337 — list all processes running on port 1337
  
• Searching
  grep pattern files — search for pattern in files
  grep -r pattern dir — search recursively for pattern in dir
  grep -rn pattern dir — search recursively for pattern in dir and show the line number found
  grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension
  command | grep pattern — search for pattern in the output of command
  find file — find all instances of file in real system
  locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find
  sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
  
• Compression
  tar cf file.tar files — create a tar named file.tar containing files
  tar xf file.tar — extract the files from file.tar
  tar czf file.tar.gz files — create a tar with Gzip compression
  tar xzf file.tar.gz — extract a tar using Gzip
  gzip file — compresses file and renames it to file.gz
  gzip -d file.gz — decompresses file.gz back to file
  
• Shortcuts
  ctrl+a — move cursor to beginning of line
  ctrl+f — move cursor to end of line
  alt+f — move cursor forward 1 word
  alt+b — move cursor backward 1 word